Modified guide rnas, crispr-ribonucleotprotein complexes and methods of use

ABSTRACT

Described herein are modified guide RNAs such as a single guide RNA including, from 5′ to 3′, a single-stranded protospacer sequence, a first complementary strand of a binding region for the Cas9 polypeptide, an aptamer that binds a biotin-binding molecule, and a second complementary strand of the binding region for the Cas9 polypeptide. Also described is an RNP complex including the modified guide RNA and a Cas9 polypeptide or active fragment thereof. Also included are methods of modifying target genes in cells using the modified guide RNAs.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.16/008,376, which claims priority to U.S. Provisional Application62/519,317 filed on Jun. 14, 2017, which is incorporated herein byreference in its entirety.

FIELD OF THE DISCLOSURE

The present disclosure is related to modified guide RNAs andCRISPR-ribonucleoprotein complexes containing the modified guide RNAsand their use in genome editing methods.

BACKGROUND

Precise editing of DNA sequences in the human genome can be used tocorrect mutations or introduce novel genetic functionality for manybiomedical purposes. Specifically, nonviral delivery of pre-formedCRISPR ribonucleoproteins (RNPs) is currently being developed forsomatic gene editing applications. RNPs combining Streptococcus pyogenesCas9 nuclease (Sp. Cas9, a high-affinity nuclease isolated from a typeII CRISPR-associated system) and a single-guide RNA (sgRNA), forexample, generate on-target DNA double strand breaks (DSBs) with littleto no off-target DNA cleavage. This break can be repaired through errorprone non-homologous end joining (NHEJ) or precise homology directedrepair (HDR), in which a template is used. Co-delivery of a nucleic aciddonor template with the Sp.Cas9 RNP (Sp.Cas9+sgRNA) is capable ofproducing precise edits at target loci through HDR of the DSB. However,variable delivery of the CRISPR system along with the donor templatesgenerates a spectrum of edits, where a majority of cells includeimprecise insertions and deletions (indels) of DNA bases from NHEJrepair of the DSB. Even when precise HDR of the DSB occurs on oneallele, there is a chance that both alleles in diploid cells are notidentically edited, resulting in imprecise edits on the other allele.Faithful writing of DNA, or scarless gene editing, within human cellsremains an outstanding challenge.

Strategies to promote precise editing include addition of smallmolecules to block NHEJ and restricting Sp. Cas9 activity to particularphases of the cell cycle, but variability and toxicity has been observedacross human cell lines when applying small molecules to promote HDR.Also, selection strategies through viral integration and excision ofdrug or cell-surface selection cassettes, flow cytometry forco-expressed fluorescent protein, or through transient drug selectioncan assist in the isolation of cells with one or two precisely-editedalleles. For all of these strategies, imprecise editing through NHEJtypically outnumbers precise HDR outcomes. None of the currentstrategies precisely control the delivery of the RNP with the donortemplate, and many resort to ‘flooding’ the cell with high Cas9expression and/or the donor template.

What is needed are new strategies for genome editing that have improvedediting fidelity.

BRIEF SUMMARY

In one aspect, a modified guide RNA, comprises

a crRNA comprising a single-stranded protospacer sequence, and a firstcomplementary strand of a binding region for the Cas9 polypeptide, and

a tracrRNA comprising, a second complementary strand of the bindingregion for the Cas9 polypeptide,

wherein the crRNA or the tracrRNA comprises an aptamer that binds abiotin-binding molecule,

wherein the crRNA and the tracrRNA hybridize through the first andsecond complementary strands of the binding region for the Cas9polypeptide.

In another aspect, a modified sg RNA comprises, from 5′ to 3′,

a single-stranded protospacer sequence,

a first complementary strand of a binding region for the Cas9polypeptide,

an aptamer that binds a biotin-binding molecule, and a secondcomplementary strand of the binding region for the Cas9 polypeptide.

In another aspect, an RNP complex comprises the modified guide RNA suchas the sgRNA and a Cas9 polypeptide or active fragment thereof.

In another aspect, a method of modifying a target gene in a cellcomprises delivering to the cell the RNP complex described above,wherein the single-stranded protospacer sequence of the modified guideRNA such as the sgRNA hybridizes to a sequence in the target gene to bemodified.

In another aspect, a method of modifying a target gene in a cellcomprises delivering to the cell the modified guide RNA described above,wherein the modified guide RNA is associated with a biotin-bindingmolecule, and wherein the single-stranded protospacer sequence of themodified guide RNA hybridizes to a sequence in the target gene to bemodified.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed incolor. Copies of this patent or patent application publication withcolor drawing(s) will be provided by the Office upon request and paymentof the necessary fee,

FIG. 1 is a schematic showing assembled ssODN-S1mplexes which arecomplexes of Sp. Cas9 protein, sgRNA with Sim aptamer, streptavidin, anda single-stranded oligodeoxynucleotide (ssODN) donor template.Sim-sgRNAs add an RNA aptamer at the first stem loop of the sgRNA thatis capable of binding streptavidin protein. A biotin-ssODN is then addedto this tertiary complex. ssODN-S1mplex particles are designed topromote homology directed repair (HDR).

FIG. 2 shows the predicted secondary structure of Sim-sgRNA. Protospacerdesignates the region that defines the sequence to target in the humangenome. Sim stem loop (coral) binds streptavidin.

FIG. 3 shows the predicted secondary structure of Sim-sgRNAs variants.

FIG. 4 shows in vitro transcription of S1m-sgRNAs compared to standardsgRNAs. Sim-sgRNAs are larger than sgRNAs due to the insertion of S1mstem loop.

FIG. 5 shows in vitro complexes of sgRNAs and streptavidin. Lane 1:Sim-sgRNA. Lane 2: streptavidin. Lane 3-5: Progressive ratios ofSim-sgRNA streptavidin. As streptavidin concentration was increased theelectrophoretic front of Sim-sgRNAs was slowed. The presence of severalbands may be due to multiple Sim-sgRNAs binding to a singlestreptavidin. Lane 6-7: Addition of streptavidin to standard sgRNAs donot shift the electrophoretic front.

FIG. 6 shows dynamic light scattering of ssODN-S1mplex (S1mplex=tertiarycomplexes of Sp.Cas9, Sim-sgRNA, and streptavidin) particle assembly.Cas9 (orange) and streptavidin (blue) proteins fail to interact when insolution together and have a hydrodynamic radius consistent withpublished data. The addition of sgRNA to Sp. Cas9 protein increases theradius of the particle to 10 nm (yellow). This radius does not changewith the addition of streptavidin (red). When Sim-sgRNAs are added toSp. Cas9 (purple), the radius is increased by a larger amount thansgRNAs, potentially due to the larger size of the Sim-sgRNA. Whenstreptavidin is added to this complex (green), a shift in size of about3 nm occurs, the size of streptavidin. A second peak at 35 nm may beassociated with multiple Cas9-S1m-sgRNA complexes connected to a singlestreptavidin.

FIG. 7 shows two representative single cell multispectral flowcytometric images of S1m-sgRNA and sgRNA transfected cells with Cas9immunohistochemistry and fluorescent streptavidin (scale bar: 10 μm).Arrowheads indicate presence of overlapping colors. Numbers in yelloware measured log Pearson correlation coefficient as determined by IDEASsoftware.

FIG. 8 shows the correlation coefficient of Cas9 immunocytochemistryfluorescent signal and streptavidin fluorescence, as measured bymultispectral image cytometry within hPSCs. Use of S1m-sgRNAsignificantly increased the correlation between the two signals(***p<10⁻⁵, Student's two-tailed t-test).

FIG. 9 shows representative confocal images of S1m-sgRNA and sgRNAtransfected cells with Cas9 immunohistochemistry and fluorescentstreptavidin (scale bar: 5 μm). Arrowheads indicate presence ofoverlapping colors.

FIG. 10 shows the correlation coefficient of Cas9 immunocytochemistryand streptavidin fluorescence inside the nuclei of transfected cells.Introduction of S1m-sgRNAs significantly increased the correlationbetween the two molecules (*p<0.05, Student's two-tailed t-test).

FIG. 11 shows in vitro tertiary complexes of S1m-sgRNA, streptavidin,and ssODN. Lanes 1-4: Components of S1m particles ran individually.Lanes 5-7: complexes of S1m-sgRNAs, streptavidin, and biotin-ssODNs.Three concentrations of ssODN were used while amount of S1m-sgRNA andstreptavidin was held constant. Major bands showing the complexation ofall three components can be seen. Elongated bands may be due todifferent stoichiometry of bio-ssODN and S1m-sgRNA connected tostreptavidin.

FIG. 12 shows in vitro tertiary complexes of S1m-sgRNA, streptavidin,and ssODN. Lanes 1-4: Components of S1m particles ran individually.Lanes 5-7: complexes of S1m-sgRNAs, streptavidin, and biotinylatedssODNs. Numbers represent relative stoichiometry between components ranon gel. Major bands showing the complexation of all three components canbe seen. Elongated bands may be due to different stoichiometry ofbiotin-ssODN and S1m-sgRNA connected to streptavidin. Lanes 8-10:complexes of S1m-sgRNAs, streptavidin, and ssODNs. ssODNs do notinterfere with the binary complex. Lane 11: complexes of streptavidinand biotin-ssODNs, with free sgRNAs. None of the typicalS1m-sgRNA-streptavidin complexes can be seen in this lane.

FIG. 13 shows gene editing via NHEJ using S1m-sgRNA RNPs. Knockout ofintegrated H2B-mCherry fluorescence in human embryonic kidney (HEK)cells. When transfected together with a plasmid encoding Sp. Cas9,S1m-sgRNAs induced ˜50% the level of NHEJ as sgRNA as measured by theloss of fluorescence (44.9% vs. 83.1%) five days post transfection.

FIG. 14 shows the ratio of precise to imprecise editing using S1mplexesformed with different S1m-sgRNA variants in hPSCs. Each S1m-sgRNAincreased the ratio of precise to imprecise editing when compared tosgRNAs. S1mplexes with S1m-sgRNA-1, and S1m-sgRNA-2 had the highestratios of precise editing.

FIG. 15 shows the ratio of precise to imprecise editing at BFP locus.ssODN-S1mplexes had an 18.4-fold higher ratio than sgRNAs and containedfour precise edits to every one indel as analyzed by deep sequencing 8days post lipofection of HEKs.

FIG. 16 shows the ratio of precise to imprecise editing at EMX1 locus.ssODN-S1mplexes had a 2.7-fold higher ratio than sgRNAs.

FIG. 17 shows the ratio of precise insertions to imprecise indels at BFPlocus in hPSCs as analyzed by deep sequencing. ssODN-S1mplexes had a9.7-fold increase in comparison to standard sgRNAs and a 7.4-foldincrease when compared with untethered ssODNs.

FIG. 18 shows the ratio of precise insertions to imprecise indels atEMX1 locus. Addition of streptavidin to S1mplex resulted in a 15-foldincrease in the ratio of precise insertions to imprecise indels.

FIGS. 19 and 20: ssODN design. Genomic sequence is denoted with blackbars. sgRNA targeting site and PAM is denoted by ‘PAM’ inside genomiclocus, while red triangles are the sgRNA cut site. ssODN length ismeasured around cut site either upstream (−) or downstream (+) as readby the reading frame. Biotin (blue hexagon) was attached to either the5′ or 3′ end of the ssODN. ssODNs were identical in sequence to eitherthe PAM or Non-PAM sequence as read in a 5′-3′ direction. RNP controlswere standard sgRNAs plus corresponding ssODN.

FIG. 19 shows absolute NHEJ (orange diamonds) and HDR percentages(purple diamonds) as a function of total reads at two different loci inhPSCs using different ssODN designs. Each symbol represents a singlereplicate analyzed by deep sequencing 4 days after nucleofection intohPSCs. HDR levels were generally higher in each replicate than NHEJlevels.

FIG. 20 shows the ratio of HDR:indel reads in deep sequencing using eachssODN combined with S1mplexes. Blue circles represent individualbiological replicates. With each ssODN, S1mplexes increased the ratio ofHDR:indel when compared to sgRNA controls but no significant trends asto symmetry, sidedness, or biotin location were observed.

FIG. 21 is a schematic of S1mplexes with quantum dot cargoes. Qdots canbe complexed with the S1mplex by a disulfide linker (Qdot-SS-S1mplex,top) or by using streptavidin covalently attached directly to thequantum dot (QdotSA-S1mplex, bottom). The quantum dot has a meandiameter of 20 nm.

FIG. 22 shows a gene editing comparison of different Qdot S1mplexes.Gene editing of HEK H2B-mCherry reporter cells five days post sorting asassayed by flow cytometry. QdotSA interferes with RNP activity, whileQdot-SS has equivalent gene editing activity as the free RNP (n=3technical replicates).

FIG. 23 shows gene-editing using various combinations of components withQdotSA. Conjugation of S1mplexes to QdotSA significantly lowers geneediting efficiency. Editing efficiency is lower even if QdotSA istransfected separately from the S1mplexes without complexation.S1m-sgRNA|QdotSA indicates complexation of S1m-sgRNA RNP withtransfection agent in a separate tube from QdotSA complexation withtransfection agent, and subsequent addition of the contents of theS1m-sgRNA tube followed immediately by addition of the QdotSA tube. 5hr. gap indicates a 5 hour culture time between transfections. Immediateapplication of the QdotSA can moderately interfere with the activity ofthe RNP, but these interference effects are abrogated if QdotSA is added5 hours later. All RNP activity is abrogated by complexation with theQdotSA (last column) (n=3 technical replicates).

FIG. 24 shows representative epifluorescence images of untransfected andQdot-SS-S1mplex transfected cells 24 hours post transfection (Scale bar:10 μm). Arrowheads indicate Qdot fluorescence in the cytoplasm.

FIG. 25 shows increased fluorescence of Qdot-S1mplex allows sorting outof quantum dot positive fractions compared to untransfected cells 24hours post transfection.

FIG. 26 shows quantum dot conjugation to S1mplex via a cleavabledisulfide linker allows fluorescent enrichment of gene-edited humancells. Increased fluorescence of Qdot-S1mplex after cleavage of thedisulfide linker allows sorting out of quantum dot positive fractionscompared to untransfected cells 24 hours post transfection (n=3biological replicates).

FIG. 27 shows a schematic of simultaneous editing at two loci strategy.HEK cells were transfected simultaneously with two S1m particles,labeled with distinct fluorophores. Editing at the BFP locus wasassociated with Red-ssODN-S1mplexes (AlexaFluor®-594 fluorophore), whileediting at the EMX1 locus was associated with Green-ssODN-S1mplexes(AlexaFluor®-488 fluorophore).

FIG. 28 shows single cells sorting for enrichment of editing at BFPlocus. In enriched S1mplex clonal populations, indels (brown) and HDR(blue) events occurred in a 1:1 ratio. In sgRNA clones, all isolatedclones either had indel or wildtype genotypes. Genotypes were assayed bySanger sequencing. No mosaic genotypes were observed.

FIG. 29 shows fluorescent S1mplexes inside the cell using confocalmicroscopy. Arrows denote Green-S1mplex both inside the nucleus andoutside the cell (Scale bar: 10 μm).

FIG. 30 shows twenty-four hours post transfection, cells were sortedinto populations that were positive for either fluorophore, both orneither. Analysis via deep sequencing was done 6 days post sorting. Top:ratio of precise (perfect sequence match to ssODN) to imprecise editing(indels) in sorted populations. Populations enriched for BFP targetedS1mplexes (Red+ and double positive) had elevated ratios up to 40 timesas many insertions as indels. Bottom: ratio of precise to impreciseediting in sorted populations. Populations enriched for EMX1 targetedS1mplexes (Red+ and double positive) had elevated ratios of preciseinsertions to indels.

FIG. 31 Off-target analysis of double positive populations using TIDE atthe top 5 off-target locations for each sgRNA. No modifications weredetected below the TIDE limit of detection (dotted line).

FIG. 32 shows an off-target analysis of sorted S1mplex populations.Off-target analysis using TIDE software at the top 5 predictedoff-target sites within the human genome at the BFP and EMX1 loci. Yaxis indicates the percentage of cells with 0 mismatches from theparental sequence (perfect matches in sequencing reads). None of thesorted S1mplex populations showed off-target effects above the limit ofdetection. The unsorted sgRNA RNP population had a small proportion ofcells that may have been edited at OT-2 of the EMX1 off-target sites.

FIG. 33 shows release of a biotin-ssODN through a photocleavable linkagehad no significant effect on HDR editing. FIG. 33a shows a biotin-ssODNthat contained a UV-cleavable linker was attached to streptavidin andS1mplex particles in order to study the potential of releasing the ssODNinside the cell to promote HDR. Lane 1: DNA standard. Lane 2:Photo-cleavable biotin-ssODN. Lane 3: standard ssODN. Lane 4: Binarycomplexes of streptavidin and photo-cleavable biotin-ssODNs. Lane 5-6:Binary complexes cleaved by either exposure to light through a DAPIfilter cube (lane 5) or exposure to a UV transilluminator (lane 6). DAPIfilter cube cleaved nearly all ssODN after 10 minutes whereastransilluminator had complete cleavage. Cleaved DNA product was the samelength as control standard ssODN. FIG. 33b shows release of biotin-ssODNby 15 minutes of light exposure through a DAPI filter cube every hourpost transfection. Levels of HDR were not significantly affected by therelease of the ssODN within the cell at any time point (n=3 biologicalreplicates).

FIG. 34 is a schematic of the structure and sequence of S1m-sgRNA-V3.This sequence removes 6 nt from the beginning of the S1m aptamer.Removal of these nucleotides simplified the secondary structure of theRNA. This modification may potentially decrease the number ofincorrectly folded and therefore inactive S1m-sgRNAs.

FIG. 35 shows the binding capability of S1m-sgRNA-1 and S1m-sgRNA-V3with streptavidin using an electrophoretic mobility shift assay (EMSA).S1m-sgRNAs or standard sgRNAs were mixed with native streptavidinprotein at the indicated ratios (w/w) and allowed to complex prior tobeing loaded on an agarose gel. Lane 1: S1m-sgRNA-1. Lane 2:S1m-sgRNA-V3. Lane 3: Streptavidin. Lane 4: 10:1S1m-sgRNA-1:Streptavidin. Lane 5: 1:1 S1m-sgRNA-1:Streptavidin. Lane 6:1:10 S1m-sgRNA-1:Streptavidin. Lane 7: 10:1 S1m-sgRNA-V3:Streptavidin.Lane 8: 1:1 S1m-sgRNA-V3:Streptavidin. Lane 9: 1:10S1m-sgRNA-V3:Streptavidin. Lane 10: sgRNA. Lane 7: 1:10sgRNA:Streptavidin.

FIG. 36 shows the induction of NHEJ using various sgRNAs. Cas9 RNPs wereformed with standard sgRNA, S1m-sgRNA-1, or S1m-sgRNA-V3 targeting thesame locus and transfected into H2b-mCherry expressing HEK cells. % NHEJwas measured by loss of fluorescence 7 days post transfection. BothS1m-sgRNA versions were less effective at creating double strand breaksrepaired by NHEJ than standard sgRNA. S1m-sgRNA-V3 induced more NHEJevents than V1 (˜3-fold higher) potentially due to simplified secondarystructure. Both S1m-sgRNA variants were still capable of creatinggenetic modifications. (n=3 technical replicates. Error bars represent±1 S.D.)

FIG. 37 shows the induction of HDR using various sgRNAs. Cas9 RNPs wereformed with standard sgRNA, S1m-sgRNA-1, or S1m-sgRNA-V3 targeting thesame locus. S1m-sgRNA-1 and V3 were also used to create S1mplexescontaining an ssODN to induce HDR at the target site. S1m-sgRNAs againformed fewer DSBs and S1m-sgRNA-V3 was more efficient at inducing NHEJthan V1. Similarly, when S1mplexes were formed using S1m-sgRNAs, V3induced higher levels of HDR than V1. However, in this replicate, ratiosof HDR:NHEJ differed from what was seen in previous experiments (n=3technical replicates. Error bars represent ±1 S.D.)

FIG. 38 shows identification of corrected Pompe iPSCs using ArrayEditplatform following transfection with fluorescent S1mplexes. Array Editenables tracking of phenotypic characteristics.

FIG. 39 shows the phenotypic difference between wildtype and Pompedisease iPSCs. Cell lines were cocultured together at the indicatedratio and evaluated for the presence of mCherry (wildtype) or DAPI(disease). Lysosome acidity was measured using LysoSensor™ Green andquantified on a per-cell basis.

FIG. 40 shows identification of corrected Pompe iPSCs. Pompe iPSCs andH9-H2b-mCherry cells were mock transfected and plated of ArrayEditplatform. Over seven days number of cells per feature was tracked andused to calculate average growth rate (bottom right). On day seven,wells were stained with LysoSensor™ Green and per cell intensity wasmeasured (top left). Data was plotted as a per-feature average. PompeiPSCs were transfected with S1mplex-ssODNs targeting diseased loci andanalyzed in the same manner as described above but with the addition ofS1mplex presence on day 1. Clones to be selected (bottom left) weredetermined by gating out the lowest average growth rate of mocktransfected cells as well as the upper intensity limit of mocktransfected Pompe iPSCs. Microfeatures with cells meeting both of thesecriteria as well as displaying S1mplex presence were selected andexpanded.

FIG. 41 shows selection of gene-corrected disease iPSCs. Sangersequencing traces of corrected cell lines. Heterozygous mutations withinthe PAM sequence show that the ssODN was used as the HDR template in alllines.

FIG. 42 shows dual S1mplexes for the precise excision of genomic DNA. a)2 sgRNAs designed in the LAMAS locus for excision of a 238 bp stretch ofgenomic DNA. B) Mixed S1m sgRNAs (1,2) with streptavidin added to HEK293s, with ratio sgRNA:streptavidin 2:1 at 50 ng/well per guide. Gelshows LAMAS locus PCR amplicon spanning both guides. Average excisionefficiency of 22% with dual S1mplexes.

The above-described and other features will be appreciated andunderstood by those skilled in the art from the following detaileddescription, drawings, and appended claims.

DETAILED DESCRIPTION

Described herein are modified guide RNAs such as sgRNAs and their RNPcomplexes with Cas9. Without being held to theory, the inventorshypothesized that some of the errors in gene editing outcomes could bereduced by preassembling RNPs with donor template or other moieties thatenable the isolation of precisely-edited cells (FIG. 1). The inventorsdesigned a strategy inspired by CRISPR display that leverages structuralstudies of the RNP to identify locations in the guide RNA sequence whereRNA aptamers could be tolerated.

The S1mplex tool described here exploits high affinity interactionsbetween a short RNA aptamer and streptavidin to promote more faithfulwriting of the human genome. In an aspect, these RNP-containingcomplexes can be assembled outside the cell to a desired stoichiometryand delivered as an all-in-one gene-editing nanoparticle together with adonor nucleic acid template. In addition, the complexes can be easilydecorated with additional moieties such as fluorophores or Qdots toenrich for edited cells. Use of these particles with a biotinylatedssODN reduced heterogeneity in delivery among RNPs and nucleic acidswithin human cells and enriches the ratio of precisely-edited toimprecisely-alleles edited alleles up to 18-fold higher than standardRNP methods, approaching a ratio of four precise edits to every oneimprecise edit. Further functionalization with a unique fluorophoreenables multiplexed editing and enrichment of precisely editedpopulations through cell sorting. Taken together, advances with theS1mplex tool generates new, chemically-defined reagents to promoteprecise editing of the human genome.

The inventors devised a strategy inspired by CRISPR display thatleverages structural studies of the RNP to identify locations in thesgRNA sequence where RNA aptamers could be tolerated (FIG. 1). ThreesgRNAs with a modification either in a stem loop of the sgRNA or at the3′ end were designed (FIG. 2), as these locations have previously beenshown to tolerate additions with a minimal loss in Cas9 bindingactivity. Separately, at each location, a perfectly complementary 10nucleotide block was added which was previously shown to aid aptameraddition to sgRNAs and a 60 nucleotide S1m aptamer, which has a strongnon-covalent interaction with streptavidin. The added sequence extendsthe sgRNA stem loop and contains two distinct bulges used for binding.We termed these new sgRNAs S1m-sgRNA-1, S1m-sgRNA-2, and S1m-sgRNA-3 inreference to their position in the sgRNA from 5′ to 3′ (FIG. 2).

CRISPR refers to the Clustered Regularly Interspaced Short PalindromicRepeats type II system used by bacteria and archaea for adaptivedefense. This system enables bacteria and archaea to detect and silenceforeign nucleic acids, e.g., from viruses or plasmids, in asequence-specific manner. In type II systems, guide RNA interacts withCas9 and directs the nuclease activity of Cas9 to target DNA sequencescomplementary to those present in the guide RNA. Guide RNA base pairswith complementary sequences in target DNA. Cas9 nuclease activity thengenerates a double-stranded break in the target DNA.

CRISPR/Cas9 is an RNP complex. CRISPR RNA (crRNA) includes a 20 baseprotospacer element that is complementary to a genomic DNA sequence aswell as additional elements that are complementary to thetransactivating RNA (tracrRNA). The tracrRNA hybridizes to the crRNA andbinds to the Cas9 protein, to provide an active RNP complex. Thus, innature, the CRISPR/Cas9 complex contains two RNA species.

sgRNA refers to a single RNA species which combines the tracrRNA and thecrRNA and is capable of directing Cas9-mediated cleavage of target DNA.An sgRNA thus contains the sequences necessary for Cas9 binding andnuclease activity and a target sequence complementary to a target DNA ofinterest (protospacer sequence). In general, in an sgRNA, the tracrRNAand the crRNA are connected by a linker loop sequence. sgRNAs arewell-known in the art. While sgRNA is generally used throughout thisdisclosure, two-part guide RNAs containing a crRNA and a tracrRNA canalso be employed.

As used herein, a guide RNA protospacer sequence refers to thenucleotide sequence of a guide RNA that binds to a target DNA sequenceand directs Cas9 nuclease activity to the target DNA locus. In someembodiments, the guide RNA protospacer sequence is complementary to thetarget DNA sequence. As described herein, the protospacer sequence of asingle guide RNA may be customized, allowing the targeting of Cas9activity to a target DNA of interest.

Any desired target DNA sequence of interest may be targeted by a guideRNA target sequence. Any length of target sequence that permitsCRISPR-Cas9 specific nuclease activity may be used in a guide RNA. Insome embodiments, a guide RNA contains a 20 nucleotide protospacersequence.

In addition to the protospacer sequence, the targeted sequence includesa protospacer adjacent motif (PAM) adjacent to the protospacer regionwhich is a sequence recognized by the CRISPR RNP as a cutting site.Without wishing to be bound to theory, it is thought that the onlyrequirement for a target DNA sequence is the presence of aprotospacer-adjacent motif (PAM) adjacent to the sequence complementaryto the guide RNA target sequence. Different Cas9 complexes are known tohave different PAM motifs. For example, Cas9 from Streptococcus pyogeneshas a NGG trinucleotide PAM motif; the PAM motif of N. meningitidis Cas9is NNNNGATT; the PAM motif of S. thermophilus Cas9 is NNAGAAW; and thePAM motif of T. denticola Cas9 is NAAAAC.

A modified guide RNA is a one-part or two-part RNA capable of directingCas-9-mediated cleavage of target DNA. A modified sg RNA is a single RNAspecies capable of directing Cas9-mediated cleavage of target DNA. Amodified sgRNA, for example, comprises sequences that provide Cas9nuclease activity, a protospacer sequence complementary to a target DNAof interest, and an aptamer that binds a biotin-binding molecule. Theinventors of the present application unexpectedly found that the linkerloop that connects the tracrRNA and the crRNA in an sgRNA can bereplaced with an aptamer that binds a biotin-binding molecule such as astreptavidin-binding aptamer. Unexpectedly, the modified sgRNAs can bindboth Cas9 protein and streptavidin, and form active RNP complexes whichinduce error-prone DNA repair less frequently than standard CRISPR-Cas9RNP complexes.

In an aspect, a modified guide RNA, comprises a crRNA comprising asingle-stranded protospacer sequence and a first complementary strand ofa binding region for the Cas9 polypeptide, and a tracrRNA comprising asecond complementary strand of the binding region for the Cas9polypeptide, wherein the crRNA or the tracrRNA comprises an aptamer thatbinds a biotin-binding molecule, wherein the crRNA and the tracrRNAhybridize through the first and second complementary strands of thebinding region for the Cas9 polypeptide.

In another aspect, the crRNA and the tracrRNA form an sgRNA, the sgRNAcomprise from 5′ to 3′,

the single-stranded protospacer sequence,

the first complementary strand of a binding region for the Cas9polypeptide,

the aptamer that binds a biotin-binding molecule, and

the second complementary strand of the binding region for the Cas9polypeptide.

More specifically, a modified sgRNA comprises, from 5′ to 3′, asingle-stranded protospacer sequence, a first complementary strand of abinding region for the Cas9 polypeptide, an aptamer that binds abiotin-binding molecule, and a second complementary strand of thebinding region of the Cas9 protein. In an embodiment, in the secondarystructure of the modified sgRNA, the stem forms a stem-loop structurewith the aptamer that binds the biotin-binding molecule. Specificmodified sgRNAs are provided in FIG. 2.

The single-stranded protospacer region can comprise 17 to 20nucleotides. Exemplary binding regions for Cas9 polypeptides comprise 10to 35 base pairs.

In an aspect, the aptamer that binds a biotin-binding molecule forms astem-loop structure. The stem portion of the stem-loop structureoptionally forms a contiguous double strand with the double-strandedbinding region for the Cas9 polypeptide. The stem portion of the aptamercan comprise 9 to 15 base pairs, while the loop comprises 30nucleotides. As shown in FIG. 2, the aptamer may contain more than onestem-loop structure. As shown in Example 9, the length of the stemportion of the aptamer is not critical and can be adjusted depending onthe application of the modified guide RNA.

Also included herein is an RNP complex comprising the modified guideRNA, e.g., sgRNA, and a Cas9 polypeptide or active fragment thereof.Exemplary modified sgRNAs include:

(SEQ ID NO: 1) NNNNNNNNNNNNNNNNNNNNGUUUAAGAGCUAUGCUGCGAAUACGAGAUGCGGCCGCCGACCAGAAUCAUGCAAGUGCGUAAGAUAGUCGCGGGUCGGCGGCCGCAUCUCGUAUUCGCAGCAUAGCAAGUUUAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU; (SEQ ID NO: 2)NNNNNNNNNNNNNNNNNNNNGUUUAAGAGCUAUGCUGGAAACAGCAUAGCAAGUUUAAAUAAGGCUAGUCCGUUAUCAACUUCGAAUACGAGAUGCGGCCGCCGACCAGAAUCAUGCAAGUGCGUAAGAUAGUCGCGGGUCGGCGGCCGCAUCUCGUAUUCGGAAAAAGUGGCACCGUGACGGUGCUUUU; or (SEQ ID NO: 3)NNNNNNNNNNNNNNNNNNNNGUUUAAGAGCUAUGCUGGAAACAGCAUAGCAAGUUUAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGUGACGGUGCCGAAUACGAGAUGCGGCCGCCGACCAGAAUCAUGCAAGUGCGUAAGAUAGUCGCGGGUCGGCGGCCGCAUCUCGUAUUCGUUUU; or (SEQ ID NO: 70)NNNNNNNNNNNNNNNNNNNNGUUUAAGAGCUAUGCUGCGAAUACGAGCCGCCGACCAGAAUCAUGCCAAGUGCGUAAGAUAGUCGCGGGUCGGCGGCUCGUAUUCGCAGCAUAGCAAGUUUAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGUGAAGUCGGUGCUUUU

A “Cas9” polypeptide is a polypeptide that functions as a nuclease whencomplexed to a guide RNA, e.g., an sgRNA or modified sgRNA. The Cas9(CRISPR-associated 9, also known as Csn1) family of polypeptides, forexample, when bound to a crRNA:tracrRNA guide or single guide RNA, areable to cleave target DNA at a sequence complementary to the sgRNAtarget sequence and adjacent to a PAM motif as described above. Cas9polypeptides are characteristic of type II CRISPR-Cas systems. The broadterm “Cas9” Cas9 polypeptides include natural sequences as well asengineered Cas9 functioning polypeptides. The term “Cas9 polypeptide”also includes the analogous Clustered Regularly Interspaced ShortPalindromic Repeats from Prevotella and Francisella 1 or CRISPR/Cpf1which is a DNA-editing technology analogous to the CRISPR/Cas9 system.Cpf1 is an RNA-guided endonuclease of a class II CRISPR/Cas system. Thisacquired immune mechanism is found in Prevotella and Francisellabacteria. Additional Class I Cas proteins include Cas3, Cas8a, Cas5,Cas8b, Cas8c, Cas 10d, Case1, Cse 2, Csy 1, Csy 2, Csy 3, GSU0054, Cas10, Csm 2, Cmr 5, Cas10, Csx11, Csx10, and Csf 1. Additional Class 2Cas9 polypeptides include Csn 2, Cas4, C2c1, C2c3 and Cas13a.

Exemplary Cas9 polypeptides include Cas9 polypeptide derived fromStreptococcus pyogenes, e.g., a polypeptide having the sequence of theSwiss-Prot accession Q99ZW2 (SEQ ID NO: 5); Cas9 polypeptide derivedfrom Streptococcus thermophilus, e.g., a polypeptide having the sequenceof the Swiss-Prot accession G3ECR1 (SEQ ID NO: 6); a Cas9 polypeptidederived from a bacterial species within the genus Streptococcus; a Cas9polypeptide derived from a bacterial species in the genus Neisseria(e.g., GenBank accession number YP_003082577; WP_015815286.1 (SEQ ID NO:7)); a Cas9 polypeptide derived from a bacterial species within thegenus Treponema (e.g., GenBank accession number EMB41078 (SEQ ID NO:8)); and a polypeptide with Cas9 activity derived from a bacterial orarchaeal species. Methods of identifying a Cas9 protein are known in theart. For example, a putative Cas9 protein may be complexed with crRNAand tracrRNA or sgRNA and incubated with DNA bearing a target DNAsequence and a PAM motif.

The term “Cas9” or “Cas9 nuclease” refers to an RNA-guided nucleasecomprising a Cas9 protein, or a fragment thereof (e.g., a proteincomprising an active, inactive, or partially active DNA cleavage domainof Cas9, and/or the gRNA binding domain of Cas9). In some embodiments, aCas9 nuclease has an inactive (e.g., an inactivated) DNA cleavagedomain, that is, the Cas9 is a nickase. Other embodiments of Cas9, bothDNA cleavage domains are inactivated. This is referred to ascatalytically-inactive Cas9, dead Cas9, or dCas9.

Functional Cas9 mutants are described, for example, in US20170081650 andUS20170152508, incorporated herein by reference for its disclosure ofCas9 mutants.

In addition, to the modified sgRNA and the Cas9 polypeptide or activefragment thereof, an RNP complex may further comprise a biotin-bindingmolecule such as an avidin such as avidin, streptavidin, or NeutrAvidin™which bind with high affinity to the aptamer that binds thebiotin-binding molecule in the modified sgRNA. Avidin, streptavidin andNeutrAvidin™ are a tetramers and each subunit can bind biotin with equalaffinity. Avidin, streptavidin and NeutrAvidin™ variants that containone, two or three biotin binding sites are also available and may beemployed in the complex.

When the RNP complex comprises a biotin-binding molecule, the complexcan further comprise a biotinylated molecule which associates with thecomplex via the biotin-binding molecule. The biotinylated molecule cantarget the RNP complex to a specific cell type, organ or tissue. Forexample, PEG-coated gold nanoparticles exhibit size-dependent in vivotoxicity; the renal clearance of quantum dots can be controlled; and theaccumulation of PEGylated silane-coated magnetic iron oxidenanoparticles has been shown to be size dependent.

In one embodiment, the biotinylated molecule is a biotinylatedoligodeoxynucleotide, such as a biotinylated donor DNA template.Homologous recombination can insert an exogenous polynucleotide sequenceinto the target nucleic acid cleavage site. An exogenous polynucleotidesequence can be called a donor polynucleotide or a donor sequence. Insome embodiments, a donor polynucleotide, a portion of a donorpolynucleotide, a copy of a donor polynucleotide, or a portion of a copyof a donor polynucleotide can be inserted into a target nucleic acidcleavage site. A donor polynucleotide can be single-stranded DNA,double-stranded DNA, RNA, or a duplex of RNA and DNA. A donorpolynucleotide can be a sequence that does not naturally occur at atarget nucleic acid cleavage site. In some embodiments, modifications ofa target nucleic acid due to NHEJ and/or HDR can lead to, for example,mutations, deletions, alterations, integrations, gene correction, genereplacement, transgene insertion, nucleotide deletion, gene disruption,and/or gene mutation. The process of integrating non-native nucleicacid(s) into genomic DNA can be referred to as “genome engineering”.

In an embodiment, the biotinylated molecule is a nanoparticle, such as aquantum dot, a gold particle, a magnetic particle, a polymericnanoparticle. In another embodiment, the biotinylated molecule is abiotinylated fluorescent dye such as Atto 425-Biotin, Atto 488-Biotin,Atto 520-Biotin, Atto-550 Biotin, Atto 565-Biotin, Atto 590-Biotin, Atto610-Biotin, Atto 620-Biotin, Atto 655-Biotin, Atto 680-Biotin, Atto700-Biotin, Atto 725-Biotin, Atto 740-Biotin, fluorescein biotin,biotin-4-fluorescein, biotin-(5-fluorescein) conjugate, andbiotin-B-phycoerythrin, Alexa Fluor® 488 biocytin, Alexa Fluor®546,Alexa Fluor® 549, lucifer yellow cadaverine biotin-X, Lucifer yellowbiocytin, Oregon green 488 biocytin, biotin-rhodamine andtetramethylrhodamine biocytin. Biotinylated molecule may also be apeptide, proteins or protein domains, specifically antibodies and Fabdomains.

In another aspect, the biotin-binding molecule can be covalently linkedto a donor polynucleotide, a nanoparticle, or a dye molecule eitherdirectly or via a linker molecule, using, for example a disulfidelinker. The bound biotin-binding molecule can then bind the aptamer ofthe modified sgRNA. Additional biotinylated donor polynucleotides,nanoparticle, contrast agent, or dye molecules can then be associatedwith the bound biotin-binding molecule. Alternatively, thebiotin-binding molecule can be associated with the biotinylated moleculeprior to adding to modified sgRNA.

Further included herein are methods of modifying a target gene, such asa target gene in a cell by contacting the cell with the RNP complexesand modified guide RNAs described herein. The cell can be from anyorganism (e.g., a bacterial cell, an archaeal cell, a cell of asingle-cell eukaryotic organism, a plant cell, an algal cell, a fungalcell (e.g., a yeast cell), a cell from an invertebrate animal, a cellfrom a vertebrate animal, or a cell from a mammal, including a cell froma human.

Also included herein is a method of modifying a target gene in a cell,comprising delivering to the cell the modified guide RNA, wherein themodified guide RNA is associated with a biotin-binding molecule, andwherein the single-stranded protospacer sequence of the modified guideRNA hybridizes to a sequence in the target gene to be modified.

In some embodiments, the present disclosure provides for methods ofmodifying a target gene in a plant. As used herein, the term “plant”refers to whole plants, plant organs, plant tissues, seeds, plant cells,seeds and progeny of the same. Plant cells include, without limitation,cells from seeds, suspension cultures, embryos, meristematic regions,callus tissue, leaves, roots, shoots, gametophytes, sporophytes, pollenand microspores. Plant parts include differentiated and undifferentiatedtissues including, but not limited to roots, stems, shoots, leaves,pollens, seeds, tumor tissue and various forms of cells and culture(e.g., single cells, protoplasts, embryos, and callus tissue).

In an embodiment, modifying the target gene increases or decreases theexpression of a gene product of the target gene.

In another embodiment, modifying the target gene comprises high-fidelityhomology-directed repair (HDR).

In another embodiment, modifying the target gene comprises the additionof a genetic functionality, or the correction of a mutation.

In yet another embodiment, modifying the target gene creates a doublestrand break (DSB) which is repaired by a non-homologous end joining(NHEJ) cell repair mechanism generating indels thereby modifying thepolynucleotide sequence of the target gene.

In a further embodiment, modifying the target gene creates a DSB whichis repaired by a homologous recombination (HDR) cell repair mechanismincorporating a donor DNA sequence thereby modifying the polynucleotidesequence of the target gene.

In an aspect, the S1m-sgRNAs described herein can be used for bialleliccorrection. Infantile-onset Pompe disease contains two distinctdeleterious mutations at different points within a single gene. In anaspect, two S1m-sgRNAs can be employed simultaneously, one forcorrection of each disease locus. As shown in Example 11, clonescontaining edits at both alleles were identified.

In another aspect, the S1m-sgRNAs described herein can be used for theexcision of genomic DNA. In an aspect, two S1m-sgRNAs can be employedsimultaneously, wherein each S1m-sgRNA targets an end of the region tobe excised. As shown in Example 12, human cells contain the properlyexcised region of genomic DNA

Delivery of polynucleotides and RNPs of the present disclosure to cells,in vitro, or in vivo, may be achieved by a number of methods known toone of skill in the art. These methods include lipofection,electroporation, nucleofection, microinjection, biolistics, liposomes,immunoliposomes, polycation or lipid:nucleic acid conjugates.Lipofection is well known and lipofection reagents are soldcommercially. Cationic and neutral lipids that are suitable forefficient receptor-recognition lipofection of polynucleotides aredescribed in the art.

Lipid:nucleic acid complexes, including targeted liposomes such asimmunolipid complexes, and the preparation of such complexes is wellknown to one of skill in the art.

Electroporation can be used to deliver the polynucleotides and RNPs ofthe present disclosure. In these methods, the polynucleotides or RNPsare mixed in an electroporation buffer with the target cells to form asuspension. This suspension is then subjected to an electrical pulse atan optimized voltage, which creates temporary pores in the phospholipidbilayer of the cell membrane, permitting charged molecules like DNA andproteins to be driven through the pores and into the cell. Reagents andequipment to perform electroporation are sold commercially.

Biolistic, or microprojectile delivery, can be used to deliver thepolynucleotides and RNPs of the present disclosure. In these methods,microprojectiles, such as gold or tungsten, are coated with thepolynucleotide by precipitation with calcium chloride, spermidine orpolyethylene glycol. The microprojectile particles are accelerated athigh speed into a cell using a device such as the BIOLISTIC® PDS-1000/HeParticle Delivery System (Bio-Rad; Hercules, Calif.).

In another embodiment, a viral vector expressing the modified guide RNAof the present disclosure, a viral vector expressing a Cas9 polypeptideand biotinylated donor DNA template (e.g., a biotinylated donor DNAtemplate), can be transfected into a cell, such as a human cell. Humancells include human pluripotent stem cell lines and primary blood cellsuch as hematopoietic stem and progenitor cells and T-cells. Onceediting has occurred in the cell line, the cells can be differentiatedand transplanted into a subject, or used for drug development.

In some embodiments, the polynucleotides of the present disclosure mayalso comprise modifications that, for example, increase stability of thepolynucleotide. Such modifications may include phosphorothioates, chiralphosphorothioates, phosphorodithioates, phosphotriesters,aminoalkylphosphotriesters, methyl and other alkyl phosphonates such as3′-alkylene phosphonates, 5′-alkylene phosphonates, chiral phosphonates,phosphinates, phosphoramidates including 3′-amino phosphoramidate andamino alkylphosphoramidates, phosphorodiamidates,thionophosphoramidates, thionoalkylphosphonates,thionoalkylphosphotriesters, selenophosphates, and boranophosphateshaving normal 3′-5′ linkages, 2-5′ linked analogs, and those havinginverted polarity wherein one or more internucleotide linkages is a 3′to 3′, a 5′ to 5′ or a 2′ to 2′ linkage. Exemplary nucleicacid-targeting polynucleotides having inverted polarity can comprise asingle 3′ to 3′ linkage at the 3′-most internucleotide linkage (i.e. asingle inverted nucleoside residue in which the nucleobase is missing orhas a hydroxyl group in place thereof). Various salts (e.g., potassiumchloride or sodium chloride), mixed salts, and free acid forms can alsobe included.

In some embodiments, the polynucleotides of the present disclosure mayalso contain other nucleic acids, or nucleic acid analogues. An exampleof a nucleic acid analogue is peptide nucleic acid (PNA).

The invention is further illustrated by the following non-limitingexamples.

EXAMPLES Methods

Cell Culture:

WA09 hESCs (WiCell, Madison, Wis.) were maintained in E8 medium onMatrigel® (WiCell) coated tissue culture polystyrene plate (BD Falcon).Cells were passaged every 3-4 days at a 1:6 ratio using Versene®solution (Life Technologies). WA09-BFP hESCs were generated throughlentiviral transduction of BFP dest clone (Addgene #71825) and sorted toensure clonal populations. After expansion, lines were sorted monthly ona BD FACS Aria to maintain expression levels.

Human embryonic kidney cells (293T) were obtained from ATCC and weremaintained between passage 15-60 in Growth medium containing DMEM (LifeTechnologies), 10% v/v FBS (WiCell), 2 mM L-Glutamine (LifeTechnologies), and 50 U/mL Penicillin-Streptomycin (Life Technologies).Cells were passaged 1:40 with Trypsin-EDTA (Life Technologies) ontoGelatin-A (Sigma) coated plates. HEK-H2B-mCherry lines were generatedthrough CRISPR-mediated insertion of a modified AAV-CAGGS-EGFP plasmid(Addgene #22212) at the AAVS safe harbor locus using gRNA AAVS1-T2(Addgene #41818). HEK-BFP lines were generated and maintained asmentioned above. All cells were maintained at 37° C. and 5% CO2.

One Pot Transcription of S1m-sgRNA:

S1m-sgRNAs were synthesized by first creating a double stranded DNAblock that encoded the sgRNA scaffold as well as the S1m aptamer. Thisscaffold was formed by overlap PCR using Phusion® High-FidelityPolymerase (New England Biolabs) according to the manufacturer'sprotocols and was placed in the thermocycler for 30 cycles of 98° C. for10 s and 72° C. for 15 s with a final extension period of 72° C. for 10min. A second primer consisting of a truncated T7 promoter, the sgRNAtarget, and homology to the S1m scaffold was then added to the scaffoldand PCR was performed again using Phusion® and placed in a thermocyclerat 98° C. for 30 s followed by 35 cycles of 98° C. for 5 s, 60° C. for10 s, and 72° C. for 15 s, with a final extension period of 72° C. for10 min. S1m PCR products were then incubated overnight at 37° C. in aHiScribe™ T7 IVT reaction (New England Biolabs) according tomanufacturer's protocol. The resulting RNA was purified using MEGAclear™Transcription Clean-Up Kit (Thermo Fisher) and quantified on aNanodrop™2000.

S1m RNP Formation:

NLS-Cas9-NLS protein (Aldevron, Madison, Wis.) was combined withS1m-sgRNAs and allowed to complex for 5 minutes with gentle mixing. Tothis complex, streptavidin (Life Technologies) was added and the mixturewas allowed to complex for an additional 5 minutes. Finally,biotin-ssODNs (Integrated DNA Technologies) were added to the tertiarycomplex and subsequently vortexed at low speed. This final mixture wasthen allowed to sit for 10 minutes to ensure complete complexation.

S1m-sgRNA and Streptavidin Binding Gel Shift Assays:

S1m-sgRNAs were heated at 75° C. for 5 min and cooled to roomtemperature for 15 min 20 pmol S1m-sgRNA was combined with streptavidinat 10:1, 1:1, and 1:10 molar ratios in a final volume of 5 μl and themixture was allowed to complex for 10 min. The S1m-sgRNA-streptavidincomplexes were run on a 1% agarose gel. Tertiary complexes wereassembled by first mixing 15 pmol each of S1m-sgRNA and streptavidin. Tothis mixture, 6, 15, or 30 pmol of ssODN was added prior to running thecomplexes through a 1% agarose gel. All gels were run using Kb+ Ladder(Invitrogen) as a molecular weight marker to allow for inter-gel sizecomparisons even when running RNA samples.

Biotin Competition Assay:

S1m-sgRNA was heated to 75° C. for 5 min and cooled to room temperature.20 pmol each S1m-sgRNA and streptavidin were complexed for 10 min. 80pmol biotin was added at 30, 20, 10, 5, and 0 min intervals prior torunning the complexes through a 1% agarose gel.

Dynamic Light Scattering:

DLS was performed using a DynaPro® NanoStar® (Wyatt Technology) usingsmall volume (4 μL) disposable cuvettes. 10 μg of each component wasadded into the cuvette and diluted as necessary with dH₂O to reach 4 μLsolution volume. In mixed component conditions, components were allowedto mix for 5 minutes while taking readings. Acquisitions were performedfor 20 seconds with a minimum of 4 acquisitions per measurement. 5measurements were performed per sample and were conducted at roomtemperature. Data was graphed as a function of percent intensity.

Quantum Dot Biotin Conjugation:

To make Qdot-SS-simplexes, amine-PEG green fluorescent quantum dots(Qdot® ITK™ 525—ThermoFisher) were reacted with a degradable dithiolbiotin linker (EZ-Link™® Sulfo-NHS-Biotin—ThermoFisher) as follows:First, 25 μl of an 8 μM Quantum dot solution in 50 mM Borate buffer weredesalted into PBS using Zeba™ desalting columns (40K MWCO—ThermoFisher)and then reacted with excess sulfoNHS-dithiol-biotin linker for 2 hoursat 4° C. with shaking. The conjugate was purified from excess linkerthrough buffer exchange in the desalting columns. Quantum dots retainedtheir fluorescence and were stored at 4° C. until use.

RNP Delivery:

HEK transfections were performed using TransIT-X2® delivery system(Mirus Bio, Madison, Wis.) according to manufacturer's protocol. 2.5×10⁵cells/cm² were seeded in a 24-well plate 24 hours prior to transfection.RNP complexes were formed as described in 25 uL of Opti-MEM™ (LifeTechnologies). 1 μg of Ca9 protein, 500 ng sgRNA, 500 ng streptavidin,and 500 ng ssODN were used. In a separate tube, 25 uL of Opti-MEM™ wascombined with 0.75 uL of TransIT-X2® reagent and allowed to mix for 5minutes. TransIT-X2® and RNP solutions were then mixed by gentlepipetting and placed aside for 15 minutes. After this incubation, 50 μLof solution were added dropwise into the well. Media was changed 24hours post transfection.

For HEK transfections involving quantum dots, Lipofectamine™ 2000 (LifeTechnologies) was used for delivery. Qdot-RNP complexes were formedaccording to the following amounts (for 24 wells: 500 ng of Ca9 protein,187.5 ng sgRNA, 187.5 ng streptavidin, 3.125 pMoles of quantum dots and3 ul Lipofectamine™ per well; a quarter of these amounts were used whentransfecting 5000 cells in 96 well plates).

All hPSC transfections were performed using the 4D-Nucleofector™ System(Lonza) in P3 solution using protocol CB150. Cells were pretreated withRho-kinase (ROCK) inhibitor (Y-27632 Selleck Chemicals) 24 hours priorto transfection. 8 μg Cas9, 3.5 μg sgRNA, 3.5 μg streptavidin, and 1 μgssODN were used to form particles as described above. Cells were thenharvested using TrypLE™ (Life Technologies) and counted. 2×10⁵ cells pertransfection were then centrifuged at 100×g for 3 minutes. Excess mediawas aspirated and cells were resuspended using 20 μL of RNP solution percondition. After nucleofection, samples were incubated in nucleocuvettesat room temperature for 15 minutes prior to plating into one well of a6-well plate containing E8 media+10 μM ROCK inhibitor. Media was changed24 hours post transfection and replaced with E8 medium.

Immunocytochemistry:

To measure correlation hPSCs were transfected with Cas9 protein andstreptavidin-AF-647. 24 hours post transfection, cells were fixed using4% PFA and incubated at room temperature for 10 minutes. Cells were thenpermeabilized using 0.05% Triton X-100 and incubated for 10 minutes.Following two washes with 5% goat serum, Cas9 antibody (Clontech#632607, 1:150) was added to cells and incubated overnight at 4° C. Thenext day, cells were rinsed twice with 5% goat serum and then incubatedwith a goat anti-rabbit secondary antibody (Santa Cruz Biotech#sc-362262, 1:500) for one hour at room temperature. Cells were thenwashed twice with PBS and mounted for imaging.

To visualize S1mplexes in the nucleus human embryonic kidney cells(HEK293T) were plated at 16,000 cells per well in an 8-well chamberslide at day 0. On day 1, 20 mL of transfection media was added to cellsin 200 μL of maintenance media. Transfection media contained 20 μLOpti-MEM® (Life Technologies), 10 pmol Streptavidin Alexa Fluor® 488conjugate (Thermo Fisher), and 0.6 μL TransIT® transfection reagent(Mirus). On day 3, cells were incubated with 1× CellMask™ PlasmaMembrane Stain (ThermoFisher) and 1× Hoechst for 10 min. Followingincubation at 37° C., cells were immediately washed with PBS and fixedin 4% paraformaldehyde (IBI Scientific) at room temperature for 15 min.Cells were analyzed using a Nikon Eclipse TI epifluorescent microscopeand a Nikon ARI confocal microscope.

Multispectral Imaging Flow Cytometry:

hPSCs were transfected and stained as described above. After staining,cells were centrifuged and resuspended in 50 μL PBS. Fluorescence wasdetected on ImageStream® X Mark II (EMD Millipore) according tomanufacture instructions. Cellular colocalization was measured by IDEASsoftware package (Amnis) using predefined colocalization wizard.

Flow Cytometry:

Flow cytometry of BFP expression and conversion to GFP was measuredusing a BD FACS Aria using the DAPI and FITC filters and analyzed usingFlowJo. Voltages were established by running wild type WA09 hPSCs aswell as WA09-BFP hPSCs. Sorting was performed on a BD FACSAria™ II witha nozzle size of 100 μm at room temperature and sorted into culturemedia.

Genomic Analysis:

DNA was isolated from cells using DNA QuickExtract™ (Epicentre, Madison,Wis.) following treatment by 0.05% trypsin-EDTA and centrifugation.QuickExtract™ solution was incubated at 65° C. for 15 minutes, 68° C.for 15 minutes, and finally 98° C. for 10 minutes. Genomic PCR wasperformed following manufacturer's instructions using AccuPrime™ HiFiTaq (Life Technologies) and 500 ng of genomic DNA. Products were thenpurified using AMPure® XP magnetic bead purification kit (BeckmanCoulter) and quantified using a Nanodrop™2000. For deep sequencing,samples were pooled and run on an Illumina HiSeg™ 2500 High Throughputat a run length of 2×125 bp or an Illumina Miseq® 2×150 bp.

Deep Sequencing Data Analysis:

A custom python script was developed to perform sequence analysis. Thepipeline starts with preprocessing, which consists of filtering out lowquality sequences and finding the defined ends of the reads. For eachsample, sequences with frequency of less than 100 were filtered from thedata. Sequences in which the reads matched with primer and reversecomplement subsequences classified as “target sequences”. Targetsequences were aligned with corresponding wildtype sequence using globalpairwise sequence alignment. Sequences that were misaligned around theexpected cut site were classified as NHEJ events while sequences thathad insertions larger that 15 bp were classified as HDR events. Thefrequency, length, and position of matches, insertions, deletions, andmismatches were all tracked in the resulting aligned sequences.

Cell Membrane Staining:

Human embryonic kidney cells (HEK293) were plated at 16,000 cells/wellin an 8-well chamber slide at day 0. On day 1, 20 μL of transfectionmedia was added to cells in 200 μL of maintenance media. Transfectionmedia contained 20 μL Opti-MEM® (Life Technologies), 400 ng StreptavidinAlexa Fluor® 488 conjugate (Thermo Fisher), and 0.6 μL TransIT®transfection reagent (Mirus). On day 3, cells were incubated with 1×CellMask™ Plasma Membrane Stain (ThermoFisher) and 1× Hoechst for 10min. Following incubation at 37° C., cells were immediately washed withPBS and fixed in 4% paraformaldehyde (IBI Scientific) at roomtemperature for 15 min. Cells were analyzed using a Nikon Eclipse TIepifluorescent microscope and a Nikon AR1 confocal microscope.

Statistics:

All error bars are shown as ±1 standard deviation. p values werecomputed using a Student's two-tailed t-test and deemed significant atα<0.05.

Nucleic Acid Sequences:

The relevant nucleic acid sequences are provided in the followingtables:

TABLE 1 Primers used to create sgRNA and Sim-sgRNAs. S1m Construct NameSequence (5′ to 3′) SEQ ID NO: S1m-sgRNA-1_FGTTTAAGAGCTATGCTGCGAATACGAGATGCGGCCGCC  8GACCAGAATCATGCAAGTGCGTAAGATAGTCGCGGGTC GGCGGCCGCATCTCGTATTCS1m-sgRNA-1_R AAAAGCACCGACTCGGTGCCACTTTTTCAAGTTGATAA  9CGGACTAGCCTTATTTAAACTTGCTATGCTGCGAATAC GAGATGCGGCCGCCGACCCG S1m ForwardTTAATACGACTCACTATAGGNNNNNNNNNNNNNNNNNN 10 NNGTTTAAGAGCTATGCTGCGARNATracR AAAAGCACCGACTCGGTGCC 11

TABLE 2 Protospacer and respective PAMs used for genomic targeting.sgRNA Name Sequence (5′ to 3′) PAM SEQ ID NO: BFP GCTGAAGCACTGCACGCCATGGG 12 (BFP → GFP) EMX1 GTCACCTCCAATGACTAGGG TGG 13 (EMX1_21) mCherryGGAGCCGTACATGAACTGAG GGG 14 (mCherry_15)

TABLE 3 Forward and reverse primers for genomic loci. Genomic SEQ SEQPrimer Forward (5′ to 3′) ID NO: Reverse (5′ to 3′) ID NO: EMX1CCATCCCCTTCTGTGAATGT 15 GGAGATTGGAGACACGGAGA 16 EMX1TCCACCTTGGCTTGGCTTTG 17 CCCTCCACCAGTACCCCAC 18 Symmetric mCherryAAGGGCGAGGAGGATAACATGG 19 TTGTACAGCTCGTCCATGCCG 20 Interior EMX1CCAATGACAAGCTTGCTAGC 21 Insertion

TABLE 4 ssODNs used to direct HDR after DSB formation. ssODN DonorSequence (5′ to 3′) SEQ ID NO: BFP → GFP NTTCATGTGGTCGGGGTAGCGGCTGAAGCACTGCACGCCAT 22GGGTCAGGGTGGTCACGAGGGTGGGCCAGGGCACCGGCA GCTTGCCGGTGGTGCAGATGAA BFP → GFP5Biotin/TCATGTGGTCGGGGTAGCGGCTGAAGCACTG 23 5PCBio NTCACGCCATGGGTCAGGGTGGTCACGAGGGTGGGCCAGGG CACCGGCAGCTTGCCGGTGGTGCAGATGAAEMX1 NT AAGCAGCACTCTGCCCTCGTGGGTTTGTGGTTGCCCACC 24GCTAGCAAGCTTGTCATTGGAGGTGACATCGATGTCCTC CCCATTGGCCTG EXM15Biotin/AAGCAGCACTCTGCCCTCGTGGGTTTGTGGT 25 5PCBio NTTGCCCACCGCTAGCAAGCTTGTCATTGGAGGTGACATCG ATGTCCTCCCCATTGGCCTG

TABLE 5Off-target sequences and corresponding genomic locus for each sgRNA used.Mismatches from protospacer are labelled in red. sgRNA Target SequenceOff-Target Sequence SEQ ID NO: PAM Locus BFP → GFP OT1GCAGAAGCACTGCAAGCCAT 27 CAG chr17: GCTGAAGCACTGCACGCCAT +39786906(SEQ ID NO: 26) OT2 TCTGAAGTGCTGCACGCCAT 28 CAG chr2: −238397265 OT3GTGGAAGCACTGCAAGCCAT 29 TGG chr7: −11228464 OT4 GGTGGAGCAGGGCACGCCAT 30CAG chr9: +109114765 OT5 GAAGAAGCACTGCACCCCAT 31 CAG chr13: −75660548EMX1 OT1 AGGACCACCAATGACTAGGG 33 CAG chr3: GTCACCTCCAATGACTAGGG−64303990 (SEQ ID NO: 32) OT2 ACCACCTGTAATGACTAGGG 34 TAG chr4:−149749778 OT3 GGAGCCTCCAGTGACTAGGG 35 GAG chr17: −38423030 OT4GTGAACTACAGTGACTAGGG 36 TGG chr8: +112210096 OT5 CTGGCCTCCAAAGACTAGGG 37GAG chr15: −75011931

TABLE 6Forward and reverse primers used to amplify off-target genomic loci.Off-Target SEQ SEQ Primer Forward (5′ to 3′) ID NO: Reverse (5′ to 3′)ID NO: BFP OT1 TTTCCTAGCAAGCAGACTCAGA 38 AGCTGTCCTTTGTCCCATTGA 39BFP OT2 TCTCCATGCCCTCCTTTCCAT 40 GGATGTAGTCCATGATCTTCCCC 41 BFP OT3TCCCAGAATGTGAAAGTGGAGG 42 CTGTGGGCTTTCCTCAGCTC 43 BFP OT4GCTGACTAACGTCCACTGCT 44 TGGACCTATGTTTTTCTTCGTCAC 45 BFP OT5AAAGTCTGTGGCCTTGTGAGA 46 AACCCTACCCCCTACCTGAA 47 EMX1 OT1TTCCCCAGGTAGTTGCTGTTC 48 TCTGCACATGTCCCAACTGTC 49 EMX1 OT2ATCCGTACCTAACCATGACCC 50 GCACAGATCTTGGTGGCTTT 51 EMX1 OT3GGCTGGGTTTCCCAAACGTA 52 CAAACTGCTGTGTTGGGTGG 53 EMX1 OT4ACTTGGAAGGGTCCACACAA 54 CCTTGAATAGAGCATTTTTCCCCA 55 EMX1 OT5TCCTACCCTTGGATGGGGTT 56 GGGCTACACGGTCCCTAAAG 57

Example 1: Design of Modified SGRNA

A novel sgRNA with a modification at the stem loop closest to the 5′ endof the sgRNA was designed (FIG. 3). This location was chosen because ithas previously been shown to tolerate additions with a minimal loss inactivity. An S1m aptamer was added, which has a strong non-covalentinteraction with streptavidin. The added S1m aptamer extends the sgRNAstem loop closest to the 5′ end and contains two distinct bulges usedfor binding. These modifications do not otherwise disrupt the predictedsgRNA secondary structure (FIG. 3). We confirmed that S1m-sgRNAs can bemade rapidly in vitro via one-pot transcription and are larger thanstandard sgRNAs when analyzed by agarose gel electrophoresis (FIG. 3).

Similar experiments were performed with sgRNAs S1m-sgRNA-1, S1m-sgRNA-2,S1m-sgRNA-3, and S1m-sgRNA-V3.

Example 2: Formation of Streptavidin and Cas9 Complexes with ModifiedsgRNA

Next, we verified the ability of S1m-sgRNAs to complex with streptavidinin vitro by combining a constant amount of S1m-sgRNA with increasingamounts of streptavidin. The electrophoretic front of the S1m-sgRNAslowed as streptavidin levels increased (FIG. 5). At the maximum amountof streptavidin, 40% of the front had slowed demonstrating the bindingof the S1m-sgRNA with streptavidin. In contrast, when the same amount ofstandard (non-S1m) sgRNA was run with streptavidin, the electrophoreticfront remained constant.

To demonstrate the ability of S1m-sgRNA-1 to complex with streptavidinand Cas9 protein simultaneously, we performed dynamic light scattering(DLS). When streptavidin and Cas9 were combined in solution, two peakswere distinct at 3.0 nm and 7.8 nm (FIG. 6), both of which match closelythe radii previously reported for each protein. We next formed Cas9 RNPswith excess standard sgRNAs and observed that the species formed werelarger than Cas9 alone and did not increase in radius with the additionof streptavidin. Excess sgRNA was not detected by DLS and was includedin the DLS studies to ensure all key components were able to assembletogether (data not shown). Additionally, these samples had a discernablepeak corresponding to the presence of streptavidin alone. RNPscontaining S1m-sgRNAs and Sp. Cas9 protein increased in radius by alarger amount than RNPs containing standard sgRNAs and Sp. Cas9 protein,likely due to the increased length of S1m-sgRNAs. When streptavidin wasadded to S1m-sgRNA RNPs, the average radius of the complex was increasedby ˜3 nm, the radius of streptavidin protein. These tertiary complexesof Sp.Cas9, S1m-sgRNA-1, and streptavidin are termed “S1mplexes”. Thesecond, larger peak in the S1mplex DLS trace is attributed to thetetrameric nature of streptavidin that can harbor up to four RNPs.

While assembly of S1mplexes in vitro is important, the maintenance ofcomplexes post-delivery is imperative to gene editing function. Todemonstrate this capability, we delivered Cas9 protein and streptavidinin combination with either sgRNAs or S1m-sgRNAs into human pluripotentstem cells (hPSCs) via nucleofection and conducted immunohistochemistryfor the two protein components. Multispectral imaging flow cytometricanalysis of single fixed cells confirmed the co-localization of the twoprotein components within hPSCs (FIG. 7). Significantly highercorrelation in the fluorescent signals from the two protein componentswere seen when S1m-sgRNA-1 was included (p<10⁻⁵, Student's two-tailedt-test FIG. 8). To gain further subcellular resolution of thesecomponents after S1mplex delivery, images obtained using confocalmicroscopy on fixed, intact hPSC cultures were analyzed usingCellProfiler for overlap between the two components within the nuclei.At 24 hours after delivery, the correlation between the fluorescentsignals arising from Cas9 and streptavidin within the nucleus wassignificantly higher when using S1m-sgRNAs than sgRNAs (p<0.05,Student's two-tailed t-test, FIG. 9,10). Together, these resultsindicate that complexes between Cas9 and streptavidin are preservedspecifically through the S1m aptamer during transfection and subsequentsubcellular trafficking such as nuclear transport.

Example 3: Formation of a Quaternary Complex with Donor DNA Template

After demonstrating the ability to form S1mplexes, we searched for amethod to combine donor DNA template with S1mplexes and form aquaternary complex. Given the strong interaction between streptavidinand biotin (K_(D)=10⁻¹⁵ M) we selected biotinylated single-strandedoligodeoxynucleotide (ssODNs) donor templates. All components(S1m-sgRNA, streptavidin, biotin-ssODN) were run alone individually on agel and compared side-by-side with standard reagents (sgRNA, ssODN) toestablish baseline migration characteristics. The biotin-ssODN ranslightly higher than the standard ssODN, presumably due to the biotinmodification (FIG. 11, 12). Tertiary complexes were formed using varyinglevels of biotin-ssODNs. The primary band displayed a higherelectrophoretic shift than either the sgRNA or ssODN alone, indicatingcomplex formation (FIG. 11, lanes 5-7). To demonstrate that allcomponents combined successfully, unmodified ssODNs were run in theplace of biotin-ssODNs. The unmodified ssODN displayed the expectedelectrophoretic shift despite the presence of the S1m-streptavidincomplex (FIG. 12, lanes 8-10). Finally, standard sgRNA was run withstreptavidin and biotin-ssODN. In this condition, the smeared band fromS1m-streptavidin binding was not observed and instead solid bandsrepresenting sgRNA and ssODN-streptavidin were present (FIG. 12, lane11).

Due to the strong interaction of biotin and streptavidin, we needed toensure that biotin did not displace S1m-sgRNA-1 already bound tostreptavidin when added in solution. To do so, we combined S1m-sgRNA-1swith streptavidin at a 1:1 molar ratio. We then added 4-fold molarexcess of biotin to occupy every binding site on each streptavidinmolecule and incubated the complex for 0, 5, 10, 20, or 30 minutes.After incubation, gel shift following electrophoresis was not differentfrom bound S1m-sgRNA: streptavidin combinations suggesting that biotindid not interfere with the S1m-streptavidin interaction at four timesthe concentrations used in this study (data not shown).

Example 4: Gene Editing Activity of S1M-sgRNAs in Human Cells

Next, we examined the ability of S1m-sgRNAs to edit genes within humancells. We created a human embryonic kidney (HEK) cell line thatconstitutively expressed blue fluorescent protein (BFP) from anintegrated transgene. DSBs produced by sgRNAs that target thefluorophore in combination with Cas9 expressed from a transfectedplasmid are repaired predominantly through NHEJ, with indel formation atthe DSB. NHEJ-mediated gene edits are expected to result in a loss ofBFP fluorescence within this HEK line. After delivery of Sim-sgRNAs anda plasmid encoding Cas9 to this HEK line, BFP expression was analyzedvia flow cytometry. All S1m-sgRNAs (1, 2, and 3) created indels atapproximately half the frequency of standard sgRNAs (data not shown).While the ˜2-fold decrease in generating indel edits is significant,such decreases in indel formation have been linked to a concomitantdecrease in off-target effects.

We also created a human embryonic kidney (HEK) cell line thatconstitutively expressed a histone 2B (H2B)-mCherry fusion proteingenerated by integrating a transgene into one chromosome at the safeharbor AAVS1 locus. DSBs produced by sgRNAs that target the mCherryfluorophore in combination with Sp. Cas9 expressed from a transfectedplasmid will be repaired predominantly though NHEJ, with indel formationat the DSB. NHEJ-mediated gene edits are expected to create a loss ofmCherry fluorescence assayed via flow cytometry. When transfected intocells, S1m-sgRNAs created NHEJ gene edits at approximately half thefrequency of standard sgRNAs, knocking out fluorescence in 45% of cellscompared to 83% loss by standard sgRNAs (FIG. 13). While the ˜2-folddecrease in generating NHEJ edits is significant, such decreases in NHEJactivity have been linked to a concomitant decrease in off-targeteffects.

Example 5: Increased HDR to Indel Ratios in Human Cells

We tested the ability of all three ssODN-S1mplexes to induce HDR in ahPSC line containing a BFP-expressing transgene that can be switched toexpress GFP through a 3 nucleotide switch (data not shown). S1mplexeswith biotin-ssODNs (ssODN-S1mplexes) were assembled using one of thethree S1m-sgRNAs and compared to standard sgRNAs and ssODN combinations.After delivery of ssODN-S1mplexes and subsequent deep sequencing ofgenomic DNA, we found that all three ssODN-S1mplexes had a higher ratioof HDR:indel editing than standard RNPs. ssODN-S1mplexes withS1m-sgRNA-1 and S1m-sgRNA-2 induced similar ratios of HDR:indel editingwhile ssODN-S1mplexes with S1m-sgRNA-3 had a slightly depressedHDR:indel ratio (FIG. 14). The decreased HDR:indel ratio found usingS1m-sgRNA-3 may have been due to the lower binding affinity of thissgRNA with streptavidin, as seen in the EMSA (data not shown). In orderto minimize the frequency of indel mutations while maximizing HDR, wedecided to use S1m-sgRNA-1 for all remaining experiments and will referto it henceforth simply as S1m-sgRNA.

With this knowledge, we then evaluated S1mplexes in multiple human celllines for their ability to generate a variety of precise nucleotidechanges. We assembled ssODN-S1mplexes to again switch BFP to GFP. Afterdelivery to HEK cells, deep sequencing revealed that the ssODN-S1mplexesenriched the ratio of precise insertions to imprecise editing 18.4-foldover standard RNPs and approached a ratio of four precise edits to everyone indel (FIG. 15). When the same experiments were conducted in hPSCs,results from flow cytometry assays were consistent with theseconclusions from deep sequencing (data not shown). Additionally, whenintroducing a 12 nucleotide insertion into the EMX1 locus²⁹ of HEKs withssODN-S1mplexes, the ratio of precise insertions to imprecise editingincreased 2.7-fold over standard sgRNA RNPs (FIG. 16 and data notshown). Taken together, this shows that ssODN-S1mplexes are able toshift the balance of editing to enrich for small, precise edits withinthe genome.

We tested the ability of this strategy to create even larger sequencechanges in hPSCs by designing an ssODN that carried a variable 18nucleotide insertion. We deep sequenced the cell population afterdelivery of ssODN-S1mplexes, again targeting the BFP and EMX1 loci. Whenstandard sgRNA RNPs were transfected with streptavidin-ssODN complexes,minimal insertion was seen with a subsequently low ratio of precise HDRto imprecise indel alleles (FIG. 17). Equivalent precise:impreciseratios were seen when standard sgRNA RNPs and ssODNs were transfected aswhen S1m-sgRNA RNPs were transfected with biotin-ssODN (withoutstreptavidin) (FIG. 17 and data not shown). However, levels of indelswere increased in the sgRNA RNP-free ssODN condition (data not shown).When the full ssODN-S1mplexes were transfected into hPSCs, HDR insertionlevels greatly increased (data not shown) as did the ratio ofprecisely-edited to imprecisely-edited alleles to 9.7-fold over standardRNP methods (FIG. 17). Again, we observed four precise edits to everyone indel with ssODN-S1mplexes at this locus. At the endogenous EMX1locus, we delivered the S1m-sgRNA RNPs with biotin-ssODNs either with orwithout streptavidin. When streptavidin was added to generate the fullssODN-S1mplex, rates of insertion increased 51-fold (data not shown),and the ratio of precise to imprecise gene-editing increased 15-fold(FIG. 18). Taken together, each component of the ssODN-S1mplex isnecessary to drive higher HDR: indel ratios within human cells.

Example 6: Design Constraints on the ssODN-S1mplex

Recent studies have reported that the design of the ssODN has asignificant effect on the rate of HDR. Accordingly, we explored variousssODN designs with ssODN-S1mplexes. Designs were limited to a 100nucleotide length for ease of synthetic synthesis, but varied asfollows: asymmetrical around the cut site, extending 30 upstream and 67bp downstream or vice-versa, either identical to the sequence containingthe PAM or the reverse complement (non-PAM), and biotinylated on eitherthe 5′ or 3′ end of the ssODN (FIGS. 19,20, left). S1mplexes containingeach unique ssODN were assembled and transfected separately intoBFP-expressing hPSCs. Four days after delivery, genomic DNA from eachcondition was collected and analyzed using deep sequencing. Under theseconditions, 2.8±2.2% of alleles in all samples were edited via HDR andNHEJ (FIG. 19, top and data not shown). We observed that neither theasymmetry, sidedness, biotin, nor location on the ssODN had asignificant effect on the HDR or indel outcomes using ssODN-S1mplexes(FIG. 19, top and data not shown). Precise editing ranged from 2-10times greater than imprecise editing (FIG. 20, top and data not shown).

We next sought to test these ssODN designs at an endogenous GAA locususing a patient-derived hPSC line that contains a pathogenic 1 bpdeletion in exon 10 on one allele. We designed sgRNAs that target onlythe mutant allele as well as ssODNs to correct the mutation to wildtypeand modify the PAM site. These ssODNs were again asymmetrical, 34 bpupstream and 66 bp downstream from the cut site, complementary to thePAM or non-PAM strand, and biotinylated at either the 5′ or 3′ end ofthe ssODN (FIG. 19, 20, bottom). At this locus ssODN-S1mplexes again hadhigher levels of precise to imprecise editing than RNPs consisting ofsgRNAs, with 3-8 precise edits occurring for every imprecise edit (FIG.20, bottom and data not shown). Consistent with the sequencing resultsat the BFP locus, absolute levels of HDR and NHEJ editing were 2.0±1.1%(FIG. 19, 20, bottom and data not shown). There was still no significantdifference between any of the ssODNs tested when complexed to theS1mplex.

Example 7: Imaging of Simplexes Transfected Cells

To facilitate isolation of the precisely-edited cells, we pursued astrategy to label the cells that received the S1mplexes by includingadditional biotinylated fluorescent cargoes. We preassembled standardstreptavidin-conjugated quantum dots (QdotSA, 20 nm diameter) withS1mplexes (QdotSA-S1mplexes, FIG. 21, bottom). After transfection ofQdotSA-S1mplexes, a subpopulation of cells contained Qdots within thecytoplasm. High-intensity green fluorescence dots were distributedvariably across the transfected cell population, indicating thatstandard transfection methods likely generate significant heterogeneityin the number of RNPs delivered to each cell. Despite the presence ofQdots in the cytoplasm, no gene editing was observed upon furtherculture and analysis within the HEK H2B-mCherry reporter cell line (FIG.22, FIG. 23). When the biotin linkage of the S1mplex to the Qdot wasmediated through a pH-sensitive disulfide linker (Qdot-SS-S1mplex, FIG.21, top), we observed a gain in gene editing activity (FIG. 22), whilethe Qdots remained largely within the cytoplasm (FIG. 24), suggestingseparation and nuclear transport of the RNP. The fluorescence from theQdot at 24 hours post transfection was utilized for fluorescenceactivated cell sorting (FACS). There was a shift in fluorescence for thewhole cell population, indicating uptake of Qdot-S1mplexes in mostcells, although to differing extents (FIG. 25). The fluorescence fromthe Qdot at 24 hours post transfection was utilized for cell sorting,and sorted cells with positive fluorescent signal were gene edited at3.7-fold higher rates versus cells transfected using standard methods(FIG. 26).

Example 8: Multiplexed Gene Editing with Simplexes

To obtain further control and refine the mutagenic spectrum ofS1mplexes, we attached a fluorescent label directly to streptavidin thatcould be used for identification during flow cytometry. We preassembledan S1m-sgRNA and biotin-ssODN targeting BFP with a streptavidin labeledwith a red fluorophore (AlexaFluor®-594) (FIG. 27) and then performed asingle cell FACS for the isolation of clones that had high fluorescenceafter delivery. Upon further cell culture, clones were analyzed bySanger sequencing for editing at the BFP locus. Of the 34 isolatedclones in the S1mplex-positive population, eight underwent HDR; eightharbored indels; and, the rest remained unedited (FIG. 28). Incomparison, when using sgRNAs, seven of the 41 isolated clones harboredindels and none were positive for HDR. Cell populations did not containmosaic gene editing, indicating that defined gene editing outcomes couldbe enriched by FACS on the S1mplex fluorescence. Using this capabilitywe tested whether if it was possible to multiplex edits usingdifferently colored S1mplexes. We thus assembled the same ssODN-S1mplextargeting BFP, termed red-ssODN-S1mplex, and separately complexed anS1m-sgRNA and biotin-ssODN targeting EMX1 with a streptavidin labeledwith a green fluorophore (AlexaFluor®-488), termed green-ssODN-S1mplex(FIG. 27). The two ssODN-S1mplexes were mixed and transfectedsimultaneously into HEKs (FIG. 29).

Twenty-four hours post transfection, we sorted cells using FACS into oneof four populations: positive for either fluorophore, both, or neither(FIG. 30). Only the top 2% of each population was taken, as we observedsome association of the fluorescent S1mplex with the cell membrane inaddition to robust fluorescent signal within the nucleus of some of thecells (FIG. 29). One-week post sort, each of the four populations wasanalyzed for editing via deep sequencing as well as by flow cytometryfor BFP editing or insert-based PCR for EMX1. Deep sequencing revealedthat editing at the EMX1 locus was increased in the presence ofgreen-ssODN-S1mplexes (Green+ and double positive fractions) (FIG. 30,and data not shown). In these populations the ratio of precise toimprecise edits increased and approached one and was 2-fold greater thanthat of the double negative fraction (data not shown). Similarly,editing at the BFP locus was increased in the Red+ and double positivefractions. As was seen in previous deep sequencing experiments, theratio of precise to imprecise edits was elevated in the presence ofS1mplexes. With the addition and sorting of fluorescent S1mplexes, theratio was greater than 10 insertions per indel (FIG. 30 and data notshown). Interestingly, the level of indels was highest in the doublenegative fraction (data not shown); this may be due to the presence ofunlabeled RNPs that did not complex with streptavidin. Results withconventional flow cytometry and PCR assays followed the same trends,consistent with these conclusions from deep sequencing data not shown).We analyzed the top 5 off-target sites for both the BFP and EMX1 sgRNAsusing TIDE³¹ in the sorted fractions as well as previous samples usedfor deep sequencing. None of the sorted populations usingssODN-S1mplexes had modifications above the TIDE limit of detection(FIG. 31, data not shown). However, using standard sgRNA RNPs, notableoff-target mutagenesis occurred at EMX1 off-target site 2 (data notshown). Taken together, the assembly of S1mplex particles with afluorescent tag can be used to create multiple, precise edits withincreased efficiency without needing multiple transfections or extendedculture.

We analyzed the top 5 off-target sites for both the BFP and EMX1 sgRNAsusing TIDE in the sorted fractions as well as previous samples used fordeep sequencing. None of the sorted populations using ssODN-S1mplexeshad modification above the limit of detection (FIG. 32). However, usingstandard sgRNA RNPs, notable off-target mutagenesis occurred at EMX1off-target site 2 (FIG. 32). Taken together, the pairing of S1mplexparticles with a fluorescent tag can be used to create multiple, preciseedits with increased efficiency without needing multiple transfectionsor extended culture.

FIG. 33 shows release of a biotin-ssODN through a photocleavable linkagehad no significant effect on HDR editing. FIG. 33a shows a biotin-ssODNthat contained a UV-cleavable linker was attached to streptavidin andS1mplex particles in order to study the potential of releasing the ssODNinside the cell to promote HDR. Lane 1: DNA standard. Lane 2:Photo-cleavable biotin-ssODN. Lane 3: standard ssODN. Lane 4: Binarycomplexes of streptavidin and photo-cleavable biotin-ssODNs. Lane 5-6:Binary complexes cleaved by either exposure to light through a DAPIfilter cube (lane 5) or exposure to a UV transilluminator (lane 6). DAPIfilter cube cleaved nearly all ssODN after 10 minutes whereastransilluminator had complete cleavage. Cleaved DNA product was the samelength as control standard ssODN. FIG. 33b shows release of biotin-ssODNby 15 minutes of light exposure through a DAPI filter cube every hourpost transfection. Levels of HDR were not significantly affected by therelease of the ssODN within the cell at any time point (n=3 biologicalreplicates).

Conclusions from Examples 1-8

The S1mplex strategy provides a straightforward, robust and modularmethod to regulate the gene editing activity of Sp.Cas9 RNPs. RNAmodification of the sgRNA with S1m can be performed readily throughshort nucleic acid synthesis methods, whereas other methods thatengineer the Cas9 protein can add challenges in protein expression,purification and stability. Our strategy could complement and addfunctionality to generate engineered variants (e.g., high fidelity,switchable, and optogenetic nucleases). Pre-assembled S1mplexes couldalso be readily manufactured to be off-the-shelf reagents withwell-defined critical quality attributes appropriate for clinical use:avidin has previously been tolerated in clinical trials and clinicalgrade Sp.Cas9 is available from several vendors.

Gene editing in human cells could be controlled by the linkages withinthe S1mplex. For the Qdot-S1mplexes, a gain of RNP activity occurredafter switching to a labile disulfide bond. Without being held totheory, it is believed that large cargoes such as Qdots (20 nm diameter)complexed with the RNP inhibit Cas9 nuclease activity. The smallerssODN-S1mplexes without labile bonds with mean diameters of 16 nm couldgenerate edits at target loci. The Qdot-S1mplex results demonstrate thatthe biotin-streptavidin linkage is strong enough to associatebiotinylated cargoes with the RNP, while disulfide bonds, which areenzymatically labile at low pH, likely dissociate the S1mplex in low pHendocytotic trafficking compartments and release the RNP from the cargoto fully recover activity. Regulating CRISPR gene editing tightlythrough the release of large cargoes could be explored with otherchemistries that generate labile cargoes upon excitation by light orheat. Such strategies could advance targeted therapy to specific areasand cell types within the body.

The site-specific complexation of the HDR donor template with the RNPthrough a biotin-streptavidin noncovalent interaction and an S1m RNAaptamer-streptavidin interaction favored precise gene editing outcomesat a ratio of ˜1-10 precise edits to each indel. Absolute levels ofprecise editing decreased as the length of insertion increased, whichhas been shown previously, and we anticipate that even higher ratios ofprecise to imprecise editing could be generated for single nucleotidechanges. 44,750 disease-associated single nucleotide or indel mutationsin the ClinVar database can be corrected, in principle, by HDR via donortemplates of 1-50 nucleotides in length. While dissociation of the RNPfrom its complexed quantum dot cargo was required for Cas9 activity,release of the biotin-ssODN through a photocleavable linkage had nosignificant effect on HDR editing (FIG. 34). Using a different chemistryin mouse cells, biotin-ssODNs could be recruited to RNPs within the cellproduced by translation of injected Cas9-avidin mRNA. Increased localconcentration of biotinylated donor template at the DSB through thestreptavidin bridge of the S1mplex could be one mechanism that increasesprecise editing. Other potential mechanisms include differentialmodification of the ssODN ends to promote strand invasion or enhancestability within the cells, and a more defined stoichiometry of the RNPto the ssODN within each cell. Further modifications to the ssODNtemplate and linkers could be used to dissect these gene editingmechanisms. The S1mplex strategy coupled with the variety ofconjugatable biotinylated reagents enables the formation of a versatiletoolkit centered around precise gene editing to advance gene editingscientific development and gene therapy.

Additional Materials and Methods

S1m-sgRNA-V3 was generated in a similar fashion but scaffold PCR wasperformed under different conditions. Phusion® PCR was performed usingthe following thermocycling protocol: 30 cycles of 98° C. for 10 s and72° C. for 15 s with a final extension period of 72° C. for 10 min.These scaffolds were then combined with the same second primer as inS1m-sgRNA-1 but cycled for 30 cycles of 98° C. for 10 s and 60° C. for10 s and 72° C. for 15 s with a final extension period of 72° C. for 10min.

LysoSensor™ Quantification.

H9 hESCs and Pompe iPSCs were harvested and counted to establish correctcell number ratios prior to being plated on glass-bottom well slides(Ibidi™). Cells were allowed to attach for 24 hours prior to analysis.Cocultures were stained with LysoSensor Green (1:1000) and Hoescht33342(1:2000) for 5 minutes followed by 2× washes with PBS. Images wereobtained using confocal microscopy (Nikon AR-1) and analyzed usingCellProfiler.

Creation of ArrayEdit Platform.

μCP was performed using previously described methods. The surfacemodification involved printing of an alkanethiol initiator to nucleatethe polymerization of hydrophilic poly(ethylene glycol) (PEG) chains.Briefly, double sided-adhesive was attached to the bottom of a standardtissue culture plate, after which a laser cutter was used to cut out thewell bottoms. Glass sheets were purchased at a size slightly smallerthan a well plate. A metal evaporator was then used to deposit a thinlayer of titanium, followed by a layer of gold onto one side of theglass sheet. Using previously described chemistry, patterns weretransferred to gold-coated glass via a polydimethylsiloxane stamp afterwhich the glass was submerged in a poly(ethylene glycol) (PEG) solutionovernight to build hydrophillic PEG chains surrounding μFeatures. Aftersubmersion, sheets were washed with deionized water to remove residualcopper deposited by the reaction and 70% ethanol to sterilize. Standardtissue culture plates with well bottoms cut out were then fastened toprocessed sheets using a custom-made alignment device.

Biallelic Correction of Pompe iPSC.

All hPSC transfections were performed using the 4D-Nucleofector™ System(Lonza) in P3 solution using protocol CA-137. Cells were pretreated withRho-kinase (ROCK) inhibitor (Y-27632 Selleck Chemicals) 24 hours priorto transfection. 50 pmol Cas9, 60 pmol sgRNA, 50 pmol streptavidin, and60 pmol ssODN were used to form particles per ssODN-S1mplex as describedabove. Cells were then harvested using TrypLE™ (Life Technologies) andcounted. 2×10⁵ cells per transfection were then centrifuged at 100×g for3 minutes. Excess media was aspirated and cells were resuspended using20 μL of RNP solution per condition. After nucleofection, samples wereincubated in nucleocuvettes at room temperature for 15 minutes prior toplating into 3×10⁴ cells per well of an ArrayEdit plate containingmTeSR1+10 μM ROCK inhibitor. Media was changed 24 hours posttransfection and replaced with mTeSR1 medium.

High-Content Image Acquisition and Analysis.

Automated microscopy was performed using a Nikon Eclipse TIepifluorescent microscope and NIS Elements Advanced Research (V4.30)software. The ND acquisition 6D module was used to establish a 20×20grid pattern such that one 10× image was taken at each μfeature andcombined in a single file. Nikon Perfect Focus was used to ensure thatall images were in the same Z-plane and in focus. Each image was thencorrected for illumination defects using CellProfiler and the number ofnuclei was determined as well as LysoSensor™ intensity and S1mplexpresence within the cell.

Dual S1mplexes for the excision of genomic DNA. Two differents1m-sgRNA-1 sequences, cutting ˜238 bps apart in the LAMAS locus weredesigned (target sequences+PAM: GTAGCCGGGGAAGCGAAGCA-GGG (SEQ ID NO: 58)and GCTCACGGACGGCTCCTACC-TGG (SEQ ID NO: 59)) and sgRNAs for thesesequences were made through in vitro transcription. One day prior totransfection, HEK 293 cells were seeded at 5,000 cells/well in a 96 wellplate. Prior to transfection, first, RNPs were formed by mixing eachS1m-sgRNA at a 1:1 molar ratio with Cas9 protein separately. DualS1mplexes were then formed by mixing the two different RNPs withstreptavidin at a 1:1:1 molar ratio. S1mplexes were then mixed withLipofectamine™ (100 ng Dual S1mplexes mixed with 0.75 uL Lipofectamine™2000 per well) and used to transfect the HEK293 cells. Three days posttransfection, cells were harvested and genomic DNA extracted asdescribed previously. A 744 bp portion of the LAMAS locus spanning bothtargets was amplified using PCR (With primers CCCCATCGTTCCATCTCCTCT (SEQID NO: 60) and CGCGGGTTCTTTTGGTATCTTG (SEQ ID NO: 61)) and bandintensities of unaffected and excised portions were used to quantifyexcision efficiency.

TABLE 7 primers S1m Construct Name SEQ ID NO: Sequence (5′ to 3′)S1m_V3_F 62 GTTTAAGAGCTATGCTGCGAATACGAGCCGCCGACCAGAATCATGCAAGTGCGTAAGATAGTCGCGGGTCGGCGGCTCGTATTC S1m_V3_R 63AAAAGCACCGACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGCGAATACGAGCCGCCGACC CG S1m1 Forward 64TTAATACGACTCACTATAGGNNNNNNNNNNNNNNNNNNNNGTTT AAGAGCTATGCTGCGA S1m-SL2_F65 GTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTCGAATACGAGATGCGGCCGCCGACCA GA S1m-SL2_R 66AAAAAAAGCACCGACTCGGTGCCACTTTTTCCGAATACGAGATGCGGCCGCCGACCCGCGACTATCTTACGCACTTGCATGATTCTGG TCGGCGGC S1m-SL3_F 67GTTTAAGAGCATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCCGA A S1m-SL3_R 68AAAAAAACGAATACGAGATGCGGCCGCCGACCCGCGACTATCTTACGCACTTGCATGATTCTGGTCGGCGGCCGCATCTCGTATTCGG CACCGACT RNATracR 69AAAAGCACCGACTCGGTGCC

TABLE 8 protospacers and respective PAMs used for genomic targeting SEQsgRNA Name ID NO: Sequence (5′ to 3′) PAM BFP (BFP → GFP) 71GCTGAAGCACTGCACGCCAT GGG mCherry 72 GGAGCCGTACATGAACTGAG GGG(mCherry_15) GAA ΔT 73 CTCGTTGTCCAGGTAGGCCC GG GAA X746 74TGGACCACCAGCTCCTGTGG GGG

Example 9: Variants of S1m-sg RNA: Variable Length of S1M Linker

We have created two different S1m-sgRNA versions that may servedifferent functions for downstream applications. Importantly, we haveshown that the exact sequence of the construct is malleable and can befine-tuned as desired. S1m-sgRNA-1 has a longer stem loop and maydemonstrate more degrees of freedom in solution or when bound to Cas9 toform an RNP. This structure may have advantages when attaching largercargoes such as additional proteins that may cause steric interferencewith Cas9 protein. Similarly S1m-sgRNA-V3 (FIG. 34) contains a shorterstem loop linking the sgRNA and S1m aptamer. This structure may beeasier to fold in to the correct secondary structure due to thedecreased complexity of the sequence and fewer binding partners for eachnucleotide in the sequence. This sequence may also be amenable tosynthetic construction methodologies that are length limited to preservefidelity of the final product

We next texted the capability of both sgRNAs to bind to streptavidinthrough an electrophoretic mobility shift assay (FIG. 35). Both sgRNAsshowed a similar shift on the gel suggesting the same binding capabilityof both aptamer constructions. This is as we expected as the coresequence and therefore secondary structure of the streptavidin bindingregion is unchanged. However, with this assay we are unable todistinguish the portion of S1m-sgRNAs that are folded correctly. BothS1m-sgRNA-1 and V3 showed similar upward mobility following EMSAsuggesting the presence of larger complexes within the solution. Incomparison, no so shift was observed when mixing sgRNAs withstreptavidin.

A core capability of the CRISPR/Cas9 system is the ability to createdouble strand breaks that are subsequently repaired by cellularmechanisms. To test this capability with S1m-sgRNAs we transfected Cas9RNPs containing an sgRNA in targeting the fluorophore (Table 8) intoH2b-mCherry expressing HEK cells and tested for the loss of fluorescenceafter 7 days. Both S1m-sgRNA variants induced fewer NHEJ events than astandard sgRNA (FIG. 36). While this loss of function is significant, itmay lend greater utility to S1m-sgRNAs in applications relating toprecise editing. In clinical settings, the high level of uncontrolledNHEJ products is undesirable. Between the two S1m-sgRNA variants, V3induced ˜3-fold higher NHEJ events than S1m-sgRNA-1. This may be due toa higher number of active sgRNAs within the transfected pool and mayalso suggest that V3 is more suitable to targeted deletion strategies.

We next tested the capabilities of both S1m-sgRNAs to induce HDR whenformed in to an ssODN-S1mplex. S1m-sgRNA-V3 again induced a higher levelof HDR when compared to S1m-sgRNA-1 (FIG. 37). However, the ratio ofprecise to imprecise mutations was decreased in this condition as thelevel of NHEJ was significantly higher than S1m-sgRNA-1. This suggeststhat S1m-sgRNA-1 may be a better choice for when only precise mutationsare desired within the target cell population.

Both S1m-sgRNA-1 and S1m-sgRNA-V3 have potential to be used in the fieldof clinical gene editing and may span different applications.S1m-sgRNA-V3 is easier to create and induces higher levels of overallediting, a feature that may be useful in ex vivo therapies. Due to thehigher cutting efficiency of S1m-sgRNA-V3, one could also envision astrategy of large deletions by tethering together two RNPs at a definedlength. S1m-sgRNA-1 in comparison is a longer aptamer and may featuremore utility for attachment of larger cargoes such as qDots or growthfactors. It generally has a lower level of overall editing efficiencyfor both HDR and NHEJ applications but may be more useful for in vivoediting where precise mutations are desired.

Example 10: Isolation of Biallelic Corrected iPSCs

We obtained an iPSC line derived from a patient afflicted withinfantile-onset Pompe disease. This cell line contains two distinctdeleterious mutations at different points within a single gene. Wecreated two fluorescent S1mplex-ssODNs containing sgRNA (Table 8) andssODNs specific to each diseased locus and transfected them into cellsprior to plating on our ArrayEdit platform (FIG. 38). ArrayEditfunctions by looking for phenotypic differences between cell colonies toenrich the proportion of selected clones that are edited. We identifiedlysosome acidity as a potential difference between healthy and diseasedcell lines that can be analyzed using image cytometry. To test thishypothesis we co-cultured WA09-H2b-mCherry expressing cells withdiseased Pompe iPSCs and stained the lysosomes with LysoSensor™ Green.LysosSensor™ Green is a dye that is preferentially trafficked to acidicorganelles and fluoresces at higher intensity at lower pH. We thenanalyzed the green intensity of each cell within the colculture usingCellProfiler and found that there was a significant difference betweenthe two populations, even when growing within the same colony (FIG. 39).

With this knowledge we mock transfected WA09 and Pompe PSCs and platedthem on ArrayEdit to obtain baseline phenotypic data. We simultaneouslytransfected Pompe iPSCs with both fluorescent S1mplex-ssODNs. Across allconditions we tracked the growth rate of colonies and seven dayspost-transfection the LysoSensor™ intensity. We also measured thepresence of each S1mplex in the corresponding condition. We again foundthat the WA09 cell colonies had a significantly higher LysoSensor™intensity than Pompe iPSCs. Importantly, we also observed Pompe iPSCcolonies that displayed intensities similar to that of the control WA09line, suggesting editing events (FIG. 40). In previous experiments weobserved that edited cell colonies may suffer a decrease in fitnesswhile editing events occurred. Accordingly, we tracked cell number ofeach colony over from day 1-7 of the experiment and plotted the averagechange in cell number over this time course. We again observed cellcolonies that grew slower than mock transfected Pompe iPSCs.Importantly, there were numerous cell colonies that fit all of thecriteria for selection for downstream analysis. These were: low growthrate, high Lysosensor™ intensity, and presence of at least one S1mplextype. After selection and Sanger sequencing we observed that we hadobtained clones that were positive for correction at both lociindividually, and most importantly one clones that contained edits atboth alleles simultaneously including mutations to the PAM site (SEQ IDNOs. 76-79; 81-84), showing the ssODN that was the used as the donor DNA(SEQ ID NOs. 75 and 80) (FIG. 41).

SEQ ID NO: 75 TGCAGCCTCTCGTTGTCCAGGTATGGCCCGGGTCCACTGCC; SEQ ID NO: 76TNCAGCCTCTCGTTGTCCAGGTATGGCCNGGNTCAATTGCT; SEQ ID NO: 77TNCAGCCTCTCGTTGTCCAGGTATGGCCCGGATCCACTGCC; SEQ ID NO: 78CTCAGACCTNTTNTTNTCAAGGTAAGGCCCGGGTCCACTGCC; SEQ ID NO: 79TNCAGCCTCTCGTTGTCCAGGTATGGCCCGGATCCACTGCC; SEQ ID NO: 80CCTGGACTGTGGACCACCAGCTCCTGTGGGGGAGGCCCT; SEQ ID NO: 81CCTGGACTGTGGACCACCAGCTCCTGTNGGGGAGGCCCT; SEQ ID NO: 82CCTGGACTGTGGACCACCAGCTCCTGTGGGGAGAGGCCCT.

Example 11: Dual Simplexes for the Excision of Genomic DNA

Dual S1mplexes containing S1m-sgRNAs targeted to 2 different spots inthe LAMAS locus were formed (FIG. 42) in order to test whether RNPstargeting 2 positions packaged into S1mplexes and transfected into HEK293 cells were able to excise the intermediate genomic sequence. Aftergenomic isolation and PCR amplification of the LAMAS, analysis (FIG. 42)showed an average excision efficiency of ˜22% of the region spanned bythe two sgRNAs in HEK293 cells, demonstrating the utility of dual guidedS1mplexes for excision purposes.

To isolate the specific S1mplexes containing only one RNP targeting eachsite, we will use HPLC (high performance liquid chromatography) toseparate out the various S1mplex species formed by random mixing ofstreptavidin and the various RNPs. We expect to be able to isolate thespecific fraction containing one RNP for each of the two sites bound toa single streptavidin. We will compare the excision efficiency of thatisolated dual S1mplexes with that of standard double sgRNAs, with andwithout a donor template for precise excision. For S1mplexes, the donorwill be biotinylated and attached to the streptavidin as part of theS1mplex. We expect the simultaneous delivery in a nanoparticle of bothRNPs as well as a donor to both increase the efficiency and precision ofexcision.

The use of the terms “a” and “an” and “the” and similar referents(especially in the context of the following claims) are to be construedto cover both the singular and the plural, unless otherwise indicatedherein or clearly contradicted by context. The terms first, second etc.as used herein are not meant to denote any particular ordering, butsimply for convenience to denote a plurality of, for example, layers.The terms “comprising”, “having”, “including”, and “containing” are tobe construed as open-ended terms (i.e., meaning “including, but notlimited to”) unless otherwise noted. Recitation of ranges of values aremerely intended to serve as a shorthand method of referring individuallyto each separate value falling within the range, unless otherwiseindicated herein, and each separate value is incorporated into thespecification as if it were individually recited herein. The endpointsof all ranges are included within the range and independentlycombinable. All methods described herein can be performed in a suitableorder unless otherwise indicated herein or otherwise clearlycontradicted by context. The use of any and all examples, or exemplarylanguage (e.g., “such as”), is intended merely to better illustrate theinvention and does not pose a limitation on the scope of the inventionunless otherwise claimed. No language in the specification should beconstrued as indicating any non-claimed element as essential to thepractice of the invention as used herein.

While the invention has been described with reference to an exemplaryembodiment, it will be understood by those skilled in the art thatvarious changes may be made and equivalents may be substituted forelements thereof without departing from the scope of the invention. Inaddition, many modifications may be made to adapt a particular situationor material to the teachings of the invention without departing from theessential scope thereof. Therefore, it is intended that the inventionnot be limited to the particular embodiment disclosed as the best modecontemplated for carrying out this invention, but that the inventionwill include all embodiments falling within the scope of the appendedclaims. Any combination of the above-described elements in all possiblevariations thereof is encompassed by the invention unless otherwiseindicated herein or otherwise clearly contradicted by context.

1. A ribonucleoprotein (RNP) complex, comprising a modified guide RNAcomprising, a crRNA comprising a single-stranded protospacer sequenceand a first complementary strand of a binding region for a Cas9polypeptide, a tracrRNA comprising a second complementary strand of thebinding region for the Cas9 polypeptide, wherein the crRNA or thetracrRNA comprises a nucleic acid aptamer that binds a biotin-bindingmolecule, wherein the crRNA and the tracrRNA hybridize through the firstand second complementary strands of the binding region for the Cas9polypeptide; the biotin-binding molecule; and the Cas9 polypeptide or anactive fragment thereof, wherein the Cas9 polypeptide or active fragmentthereof is active for guide RNA binding, and has an active, inactive orpartially inactive nuclease domain.
 2. The RNP complex of claim 1,wherein the biotin-binding molecule has one, two or four biotin bindingsites, and wherein the biotin-binding molecule optionally comprises afluorescent label.
 3. The RNP complex of claim 1, further comprising abiotinylated molecule.
 4. The RNP complex of claim 3, wherein thebiotinylated molecule is a biotinylated donor polynucleotide.
 5. The RNPcomplex of claim 4, wherein the biotinylated donor polynucleotidecomprises single-stranded DNA, double-stranded DNA, RNA, or a duplex ofRNA and DNA.
 6. The RNP complex of claim 4, wherein the donorpolynucleotide includes a mutation, deletion, alteration, integration,gene correction, gene replacement, transgene insertion, nucleotidedeletion, gene disruption, and/or gene mutation in a target nucleicacid.
 7. The RNP complex of claim 3, wherein the biotinylated moleculecomprises a biotinylated nanoparticle, dye, contrast agent, or peptide.8. The RNP complex of claim 7, wherein the nanoparticle is a quantumdot, a gold particle, a magnetic particle, or a polymeric nanoparticle.9. The RNP complex of claim 4, wherein the biotin-binding molecule iscovalently linked to the donor polynucleotide, either directly or via alinker molecule.
 10. The RNP complex of claim 9, wherein the donorpolynucleotide comprises single-stranded DNA, double-stranded DNA, RNA,or a duplex of RNA and DNA.
 11. The RNP complex of claim 10, wherein thedonor polynucleotide includes a mutation, deletion, alteration,integration, gene correction, gene replacement, transgene insertion,nucleotide deletion, gene disruption, and/or gene mutation in a targetnucleic acid.
 12. A method of modifying a target nucleic acid in a cell,comprising delivering to the cell an RNP complex, the RNP complexcomprising a crRNA comprising a single-stranded protospacer sequence anda first complementary strand of a binding region for a Cas9 polypeptide,a tracrRNA comprising a second complementary strand of the bindingregion for the Cas9 polypeptide, wherein the crRNA or the tracrRNAcomprises a nucleic acid aptamer that binds a biotin-binding molecule,wherein the crRNA and the tracrRNA hybridize through the first andsecond complementary strands of the binding region for the Cas9polypeptide; the biotin-binding molecule; and the Cas9 polypeptide or anactive fragment thereof, wherein the Cas9 polypeptide or active fragmentthereof is active for guide RNA binding, and has an active, inactive orpartially inactive nuclease domain.
 13. The method of claim 12, whereinmodifying the target nucleic acid increases or decreases expression of agene product of the target nucleic acid.
 14. The method of claim 12,further comprising delivering a donor polynucleotide to the cell, andwherein modifying the target nucleic acid comprises homology-directedrepair (HDR).
 15. The method of claim 12, further comprising deliveringa donor polynucleotide to the cell, and wherein modifying the targetnucleic acid comprises addition of a genetically encoded functionality,or correction of a mutation in the target nucleic acid.
 16. The methodof claim 12, wherein modifying the target nucleic acid creates a doublestrand break (DSB) which is repaired by a non-homologous end joining(NHEJ) cell repair mechanism generating indels thereby modifying thepolynucleotide sequence of the target nucleic acid.
 17. The method ofclaim 12, further comprising delivering a donor polynucleotide to thecell, and wherein modifying the target nucleic acid creates a DSB whichis repaired by a HDR cell repair mechanism incorporating a donor DNAsequence thereby modifying the polynucleotide sequence of the targetnucleic acid.
 18. The method of claim 12, further comprising deliveringa biotinylated molecule, wherein the biotinylated molecule targets theRNP complex to a specific cell type, organ or tissue.
 19. A method ofmodifying a target nucleic acid in a cell, comprising delivering to thecell two RNP complexes, wherein each RNP complex comprises a crRNAcomprising a single-stranded protospacer sequence and a firstcomplementary strand of a binding region for a Cas9 polypeptide, atracrRNA comprising a second complementary strand of the binding regionfor the Cas9 polypeptide, wherein the crRNA or the tracrRNA comprises anucleic acid aptamer that binds a biotin-binding molecule, wherein thecrRNA and the tracrRNA hybridize through the first and secondcomplementary strands of the binding region for the Cas9 polypeptide;the biotin-binding molecule; and the Cas9 polypeptide or an activefragment thereof, wherein the Cas9 polypeptide or active fragmentthereof is active for guide RNA binding, and has an active, inactive orpartially inactive nuclease domain.
 20. The method of claim 19, furthercomprising delivering a donor polynucleotide to the cell, wherein thedonor polynucleotide comprises a gene correction relative to thesequence of the target nucleic acid, thereby providing multiple alleliccorrection of the target nucleic acid, or excision of target DNA fromthe target nucleic acid.
 21. The method of claim 19, further comprisingdelivering a donor polynucleotide to the cell, wherein the donorpolynucleotide comprises a gene correction relative to the sequence ofthe target nucleic acid, thereby providing multiple allelic correctionof the target nucleic acid.
 22. The method of claim 19, whereinmodifying the target nucleic acid provides excision of genomic DNA. 23.The method of claim 19, wherein each RNP complex further comprises abiotinylated molecule.
 24. A method of modifying a target nucleic acidin a cell, the cell comprising a Cas9 polypeptide, wherein the Cas9polypeptide is active for guide RNA binding, and has an active, inactiveor partially inactive nuclease domain, the method comprising deliveringto the cell a modified guide RNA, the modified guide RNA comprising, acrRNA comprising a single-stranded protospacer sequence and a firstcomplementary strand of a binding region for a Cas9 polypeptide, atracrRNA comprising a second complementary strand of the binding regionfor the Cas9 polypeptide, wherein the crRNA or the tracrRNA comprises anucleic acid aptamer that binds a biotin-binding molecule, wherein thecrRNA and the tracrRNA hybridize through the first and secondcomplementary strands of the binding region for the Cas9 polypeptide;wherein the modified guide RNA is associated with the biotin-bindingmolecule; and wherein the single-stranded protospacer sequence of themodified guide RNA hybridizes to a sequence in the target nucleic acidto be modified.
 25. The method of claim 24, wherein two modified guideRNAs are delivered to the cell, and wherein each of the modified guideRNAs hybridizes to a different nucleic acid sequence.
 26. The method ofclaim 24, further comprising delivering a donor polynucleotide to thecell, wherein the donor polynucleotide comprises a gene correctionrelative to the sequence of the target nucleic acid, thereby providingmultiple allelic correction of the target nucleic acid, or excision oftarget DNA from the target nucleic acid.
 27. A kit comprising a modifiedguide RNA, the modified guide RNA comprising, a crRNA comprising asingle-stranded protospacer sequence and a first complementary strand ofa binding region for a Cas9 polypeptide, a tracrRNA comprising a secondcomplementary strand of the binding region for the Cas9 polypeptide,wherein the crRNA or the tracrRNA comprises a nucleic acid aptamer thatbinds a biotin-binding molecule, wherein the crRNA and the tracrRNAhybridize through the first and second complementary strands of thebinding region for the Cas9 polypeptide; a biotin-binding molecule; aCas9 polypeptide, and a biotinylated molecule.
 28. A method of modifyinga target nucleic acid in a cell, comprising delivering to the cell avector expressing a modified guide RNA, a vector expressing a Cas9polypeptide, an avidin, and a biotinylated donor DNA template, themodified guide RNA comprising, a crRNA comprising a single-strandedprotospacer sequence and a first complementary strand of a bindingregion for a Cas9 polypeptide, a tracrRNA comprising a secondcomplementary strand of the binding region for the Cas9 polypeptide,wherein the crRNA or the tracrRNA comprises a nucleic acid aptamer thatbinds a biotin-binding molecule, wherein the crRNA and the tracrRNAhybridize through the first and second complementary strands of thebinding region for the Cas9 polypeptide wherein the single-strandedprotospacer sequence of the modified guide RNA hybridizes to a sequencein the target nucleic acid to be modified.
 29. The method of claim 28,wherein the cell is a human cell.
 30. The method of claim 29, whereinthe human cell is a human pluripotent stem cell line, or a primary bloodcell.